The physiological potential of anammox bacteria as revealed by their core genome structure

Abstract We present here the second complete genome of anaerobic ammonium oxidation (anammox) bacterium, Candidatus (Ca.) Brocadia pituitae, along with those of a nitrite oxidizer and two incomplete denitrifiers from the anammox bacterial community (ABC) metagenome. Although NO2- reduction to NO is considered to be the first step in anammox, Ca. B. pituitae lacks nitrite reductase genes (nirK and nirS) responsible for this reaction. Comparative genomics of Ca. B. pituitae with Ca. K. stuttgartiensis and six other anammox bacteria with nearly complete genomes revealed that their core genome structure contains 1,152 syntenic orthologs. But nitrite reductase genes were absent from the core, whereas two other Brocadia species possess nirK and these genes were horizontally acquired from multiple lineages. In contrast, at least 5 paralogous hydroxylamine oxidoreductase genes containing candidate ones (hao2 and hao3) encoding another nitrite reductase were observed in the core. Indeed, these two genes were also significantly expressed in Ca. B. pituitae as in other anammox bacteria. Because many nirS and nirK genes have been detected in the ABC metagenome, Ca. B. pituitae presumably utilises not only NO supplied by the ABC members but also NO and/or NH2OH by self-production for anammox metabolism.

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Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes

F1000Research ◽

10.12688/f1000research.2-63.v1 ◽

2013 ◽

Vol 2 ◽

pp. 63 ◽

Cited By ~ 5

Author(s):

Michel A Marin ◽

Ana Carolina P Vicente

Keyword(s):

Core Genome ◽

Position Effect ◽

Genome Structure ◽

Enrichment Analysis ◽

Gene Clusters ◽

Gene Cassette ◽

Etiologic Agent ◽

Functional Genes ◽

The Core ◽

Core Genes

Background: Vibrio cholerae, the etiologic agent of cholera, is indigenous to aquatic environments. The V. cholerae genome consists of two chromosomes; the smallest of these harbors a large gene capture and excision system called the superintegron (SI), of ~120 kbp. The flexible nature of the SI that results from gene cassette capture, deletion and rearrangement is thought to make it a hotspot of V. cholerae diversity, but beyond the basic structure it is not clear if there is a core genome in the SI and if so how it is structured. The aim of this study was to explore the core genome structure and the differences in gene content among strains of V. cholerae.Methods: From the complete genomes of seven V. cholerae and one Vibrio mimicus representative strains, we recovered the SI sequences based on the locations of the structural gene IntI4 and the V. cholerae repeats. Analysis of the pangenome, including cluster analysis of functional genes, pangenome profile analysis, genetic variation analysis of functional genes, strain evolution analysis and function enrichment analysis of gene clusters, was performed using a pangenome analysis pipeline in addition to the R scripts, splitsTree4 and genoPlotR.Results and conclusions: Here, we reveal the genetic architecture of the V. cholerae SI. It contains eight core genes when V. mimicus is included and 21 core genes when only V. cholerae strains are considered; many of them are present in several copies. The V. cholerae SI has an open pangenome, which means that V. cholerae may be able to import new gene cassettes to SI. The set of dispensable SI genes is influenced by the niche and type species. The core genes are distributed along the SI, apparently without a position effect.

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Nitrogen removal during the cold season by constructed floating wetlands planted with Oenanthe javanica

Marine and Freshwater Research ◽

10.1071/mf17156 ◽

2018 ◽

Vol 69 (5) ◽

pp. 635 ◽

Cited By ~ 5

Author(s):

Penghe Wang ◽

Nasreen Jeelani ◽

Jie Zuo ◽

Hui Zhang ◽

Dehua Zhao ◽

...

Keyword(s):

Waste Water ◽

Nitrogen Removal ◽

Nitrite Reductase ◽

Waste Water Treatment ◽

Microbial Community Composition ◽

Cold Season ◽

Anammox Bacteria ◽

Ammonium Oxidation ◽

Oenanthe Javanica ◽

Floating Wetlands

Constructed floating wetlands (CFWs) are used to treat waste waters of various origins either alone or as part of waste water treatment trains. The aim of the present study was to determine the extent of nitrogen removal by CFWs planted with Oenanthe javanica (Blume) DC. at low temperatures (<10°C) and whether CFWs with vesuvianite as a substrate perform better than those without substrate. A batch model was used, with CFWs planted with O. javanica (Tc), CFWs without O. javanica (Ts), CFWs without substrate (Tp) and floating mats only (To) as a control. The average removal rates of NH4+-N, NO3–-N and total nitrogen were 78.3, 44.4 and 49.7% respectively in Tc; 72.0, 40.0 and 39.5% respectively in Ts; and 73.1, 33.7 and 44.0% respectively in Tp. In addition to a gradual increase in chemical oxygen demand during the experimental period, Tc had higher microbial richness and diversity, as well as a higher abundance of bacteria, archaea, anaerobic ammonium oxidation (Anammox) bacteria and key genes (ammonia mono-oxygenase, amoA, nitrous oxide reductase, nosZ, dissimilatory cd1-containing nitrite reductase, nirS, and dissimilatory copper-containing nitrite reductase, nirK) involved in nitrogen metabolism in the substrate than Ts. Further analysis of microbial community composition revealed a difference at multiple taxonomic levels among different systems. These results demonstrate the positive roles of O. javanica and vesuvianite in CFWs in nitrogen removal from waste water during the cold season (mean water temperature <10°C).

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Structural Basis of Biological NO Generation by Octaheme Oxidoreductases

Journal of Biological Chemistry ◽

10.1074/jbc.m113.525147 ◽

2013 ◽

Vol 289 (3) ◽

pp. 1228-1242 ◽

Cited By ~ 54

Author(s):

Wouter J. Maalcke ◽

Andreas Dietl ◽

Sophie J. Marritt ◽

Julea N. Butt ◽

Mike S. M. Jetten ◽

...

Keyword(s):

Structural Basis ◽

Anammox Bacteria ◽

Anammox Bacterium ◽

Biological Functions ◽

Fixed Nitrogen ◽

Hydroxylamine Oxidoreductase ◽

No Formation ◽

Oxidizing Power ◽

Domains Of Life

Nitric oxide is an important molecule in all domains of life with significant biological functions in both pro- and eukaryotes. Anaerobic ammonium-oxidizing (anammox) bacteria that contribute substantially to the release of fixed nitrogen into the atmosphere use the oxidizing power of NO to activate inert ammonium into hydrazine (N2H4). Here, we describe an enzyme from the anammox bacterium Kuenenia stuttgartiensis that uses a novel pathway to make NO from hydroxylamine. This new enzyme is related to octaheme hydroxylamine oxidoreductase, a key protein in aerobic ammonium-oxidizing bacteria. By a multiphasic approach including the determination of the crystal structure of the K. stuttgartiensis enzyme at 1.8 Å resolution and refinement and reassessment of the hydroxylamine oxidoreductase structure from Nitrosomonas europaea, both in the presence and absence of their substrates, we propose a model for NO formation by the K. stuttgartiensis enzyme. Our results expand the understanding of the functions that the widespread family of octaheme proteins have.

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Nitrogen isotope effects can be used to diagnose N transformations in wastewater anammox systems

Scientific Reports ◽

10.1038/s41598-021-87184-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Paul M. Magyar ◽

Damian Hausherr ◽

Robert Niederdorfer ◽

Nicolas Stöcklin ◽

Jing Wei ◽

...

Keyword(s):

Isotope Effect ◽

Isotope Composition ◽

Isotope Effects ◽

Nitrogen Isotope ◽

Anammox Bacteria ◽

Ammonium Oxidation ◽

Experimental Conditions ◽

N Transformations ◽

Natural Systems ◽

Inverse Isotope Effect

AbstractAnaerobic ammonium oxidation (anammox) plays an important role in aquatic systems as a sink of bioavailable nitrogen (N), and in engineered processes by removing ammonium from wastewater. The isotope effects anammox imparts in the N isotope signatures (15N/14N) of ammonium, nitrite, and nitrate can be used to estimate its role in environmental settings, to describe physiological and ecological variations in the anammox process, and possibly to optimize anammox-based wastewater treatment. We measured the stable N-isotope composition of ammonium, nitrite, and nitrate in wastewater cultivations of anammox bacteria. We find that the N isotope enrichment factor 15ε for the reduction of nitrite to N2 is consistent across all experimental conditions (13.5‰ ± 3.7‰), suggesting it reflects the composition of the anammox bacteria community. Values of 15ε for the oxidation of nitrite to nitrate (inverse isotope effect, − 16 to − 43‰) and for the reduction of ammonium to N2 (normal isotope effect, 19–32‰) are more variable, and likely controlled by experimental conditions. We argue that the variations in the isotope effects can be tied to the metabolism and physiology of anammox bacteria, and that the broad range of isotope effects observed for anammox introduces complications for analyzing N-isotope mass balances in natural systems.

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A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

Journal of Bacteriology ◽

10.1128/jb.01202-08 ◽

2008 ◽

Vol 191 (1) ◽

pp. 91-99 ◽

Cited By ~ 115

Author(s):

Marc Deloger ◽

Meriem El Karoui ◽

Marie-Agnès Petit

Keyword(s):

Dna Sequences ◽

Dna Content ◽

Core Genome ◽

Biological Diversity ◽

Bacterial Species ◽

Genomic Distance ◽

The Core ◽

Intraspecies Diversity ◽

Genome Level ◽

Definition Of

ABSTRACT The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

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Enhanced Nitrogen Removal from Domestic Wastewater by Partial-Denitrification/Anammox in an Anoxic/Oxic Biofilm Reactor

Processes ◽

10.3390/pr10010109 ◽

2022 ◽

Vol 10 (1) ◽

pp. 109

Author(s):

Yu Huang ◽

Yongzhen Peng ◽

Donghui Huang ◽

Jiarui Fan ◽

Rui Du

Keyword(s):

Nitrogen Removal ◽

Oxygen Demand ◽

Domestic Wastewater ◽

Biofilm Reactor ◽

Anammox Bacteria ◽

Stable Operation ◽

Ammonium Oxidation ◽

N Accumulation ◽

Carbon Demand ◽

Oxidation Efficiency

A partial-denitrification coupling with anaerobic ammonium oxidation (anammox) process (PD/A) in a continuous-flow anoxic/oxic (A/O) biofilm reactor was developed to treat carbon-limited domestic wastewater (ammonia (NH4+-N) of 55 mg/L and chemical oxygen demand (COD) of 148 mg/L in average) for about 200 days operation. Satisfactory NH4+-N oxidation efficiency above 95% was achieved with rapid biofilm formation in the aerobic zone. Notably, nitrite (NO2−-N) accumulation was observed in the anoxic zone, mainly due to the insufficient electron donor for complete nitrate (NO3−-N) reduction. The nitrate-to-nitrite transformation ratio (NTR) achieved was as high as 64.4%. After the inoculation of anammox-enriched sludge to anoxic zones, total nitrogen (TN) removal was significantly improved from 37.3% to 78.0%. Anammox bacteria were effectively retained in anoxic biofilm utilizing NO2−-N produced via the PD approach and NH4+-N in domestic wastewater, with the relative abundance of 5.83% for stable operation. Anammox pathway contributed to TN removal by a high level of 38%. Overall, this study provided a promising method for mainstream nitrogen removal with low energy consumption and organic carbon demand.

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To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2020.0475 ◽

2021 ◽

Vol 377 (1842) ◽

Author(s):

Jorge A. Moura de Sousa ◽

Eduardo P. C. Rocha

Keyword(s):

Escherichia Coli ◽

Molecular Mechanisms ◽

Core Genome ◽

Mobile Genetic Elements ◽

Abundance Distribution ◽

Theme Issue ◽

Genetic Elements ◽

The Core ◽

Antagonistic Interactions ◽

Variable Genes

Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage satellites. The molecular mechanisms used by satellites to hijack phages are sometimes understood in great detail, but the origins, abundance, distribution and composition of these elements are poorly known. Here, we show that P4-like elements are present in more than 30% of the genomes of Enterobacterales, and in almost half of those of Escherichia coli , sometimes in multiple distinct copies. We identified over 1000 P4-like elements with very conserved genetic organization of the core genome and a few hotspots with highly variable genes. These elements are never found in plasmids and have very little homology to known phages, suggesting an independent evolutionary origin. Instead, they are scattered across chromosomes, possibly because their integrases are often exchanged with other elements. The rooted phylogenies of hijacking functions are correlated and suggest longstanding coevolution. They also reveal broad host ranges in P4-like elements, as almost identical elements can be found in distinct bacterial genera. Our results show that P4-like phage satellites constitute a very distinct, widespread and ancient family of mobile genetic elements. They pave the way for studying the molecular evolution of antagonistic interactions between phages and their satellites. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

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Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes

PLoS ONE ◽

10.1371/journal.pone.0248054 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248054

Author(s):

Jaqueline Raquel de Almeida ◽

Diego Mauricio Riaño Pachón ◽

Livia Maria Franceschini ◽

Isaneli Batista dos Santos ◽

Jessica Aparecida Ferrarezi ◽

...

Keyword(s):

Mitochondrial Genome ◽

Transmembrane Protein ◽

Genome Structure ◽

Rust Fungi ◽

Mitochondrial Genomes ◽

Phylogenomic Analysis ◽

The Core ◽

Mtdna Sequence ◽

Austropuccinia Psidii

Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shaping of the rust mitochondrial genome structure. The mtDNAs from rust fungi are highly syntenic. Phylogenetic inferences with 14 concatenated mitochondrial proteins encoded by the core genes placed A. psidii according to phylogenetic analysis based on 18S rDNA. Interestingly, cox1, the gene with the greatest number of introns, provided phylogenies not congruent with the core set. For the first time, we identified the proteins encoded by three A. psidii ncORFs using proteomics analyses. Also, the orf208 encoded a transmembrane protein repressed during in vitro morphogenesis. To the best of our knowledge, we presented the first report of a complete mtDNA sequence of a member of the family Sphaerophragmiacea.

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