scholarly journals “CandidatusNitrosotenuis aquarius,” an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter

2018 ◽  
Vol 84 (19) ◽  
Author(s):  
Laura A. Sauder ◽  
Katja Engel ◽  
Chien-Chi Lo ◽  
Patrick Chain ◽  
Josh D. Neufeld
Keyword(s):  
Genome Sequence ◽  
Ammonia Oxidation ◽  
Waste Product ◽  
Optimal Growth ◽  
Protein Glycosylation ◽  
Ammonia Toxicity ◽  
Ammonia Oxidizing Bacteria ◽  
Common Belief ◽  
Content Type ◽  
Group I

ABSTRACTAmmonia is a metabolic waste product excreted by aquatic organisms that causes toxicity when it accumulates. Aquaria and aquaculture systems therefore use biological filters that promote the growth of nitrifiers to convert ammonia to nitrate. Ammonia-oxidizing bacteria (AOB) have been isolated from aquarium biofilters and are available as commercial supplements, but recent evidence suggests that ammonia-oxidizing archaea (AOA) are abundant in aquarium biofilters. In this study, we report the cultivation and closed genome sequence of the novel AOA representative “CandidatusNitrosotenuis aquarius,” which was enriched from a freshwater aquarium biofilter. “Ca. Nitrosotenuis aquarius” oxidizes ammonia stoichiometrically to nitrite with a concomitant increase in thaumarchaeotal cells and a generation time of 34.9 h. “Ca. Nitrosotenuis aquarius” has an optimal growth temperature of 33°C, tolerates up to 3 mM NH4Cl, and grows optimally at 0.05% salinity. Transmission electron microscopy revealed that “Ca. Nitrosotenuis aquarius” cells are rod shaped, with a diameter of ∼0.4 μm and length ranging from 0.6 to 3.6 μm. In addition, these cells possess surface layers (S-layers) and multiple proteinaceous appendages. Phylogenetically, “Ca. Nitrosotenuis aquarius” belongs to the group I.1aThaumarchaeota, clustering with environmental sequences from freshwater aquarium biofilters, aquaculture systems, and wastewater treatment plants. The complete 1.70-Mbp genome contains genes involved in ammonia oxidation, bicarbonate assimilation, flagellum synthesis, chemotaxis, S-layer production, defense, and protein glycosylation. Incubations with differential inhibitors indicate that “Ca. Nitrosotenuis aquarius”-like AOA contribute to ammonia oxidation within the aquarium biofilter from which it originated.IMPORTANCENitrification is a critical process for preventing ammonia toxicity in engineered biofilter environments. This work describes the cultivation and complete genome sequence of a novel AOA representative enriched from a freshwater aquarium biofilter. In addition, despite the common belief in the aquarium industry that AOB mediate ammonia oxidation, the present study suggests anin siturole for “Ca. Nitrosotenuis aquarius”-like AOA in freshwater aquarium biofilters.

scholarly journals Ecophysiological Characterization of Ammonia-Oxidizing Archaea and Bacteria from Freshwater

2012 ◽  
Vol 78 (16) ◽  
pp. 5773-5780 ◽  
Author(s):  
Elizabeth French ◽  
Jessica A. Kozlowski ◽  
Maitreyee Mukherjee ◽  
George Bullerjahn ◽  
Annette Bollmann
Keyword(s):  
Growth Rates ◽  
Ammonia Oxidation ◽  
Light Exposure ◽  
Enrichment Culture ◽  
Ammonia Oxidizing Bacteria ◽  
Content Type ◽  
Ammonia Oxidizing Archaea ◽  
Group I ◽  
Nitrosomonas Oligotropha

ABSTRACTAerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with “CandidatusNitrosoarchaeum koreensis” and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from theNitrosomonas oligotrophagroup (Nitrosomonascluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail.

scholarly journals Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil

2011 ◽  
Vol 77 (24) ◽  
pp. 8635-8647 ◽  
Author(s):  
Man-Young Jung ◽  
Soo-Je Park ◽  
Deullae Min ◽  
Jin-Seog Kim ◽  
W. Irene C. Rijpstra ◽  
...  
Keyword(s):  
16S Rrna ◽  
Agricultural Soil ◽  
Ammonia Oxidizing Bacteria ◽  
Sequence Comparisons ◽  
Soil Nitrification ◽  
Content Type ◽  
Group I ◽  
Single Sequence

ABSTRACTSoil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizingArchaeafrom soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescencein situhybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaealamoAgenes featured a single sequence each. No bacterialamoAgenes could be detected by PCR. A [13C]bicarbonate assimilation assay showed stoichiometric incorporation of13C intoArchaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to “CandidatusNitrosopumilus maritimus” revealed 96.9% 16S rRNA and 89.2%amoAgene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N2O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated “CandidatusNitrosoarchaeum koreensis.”

scholarly journals A Mesophilic, Autotrophic, Ammonia-Oxidizing Archaeon of Thaumarchaeal Group I.1a Cultivated from a Deep Oligotrophic Soil Horizon

2014 ◽  
Vol 80 (12) ◽  
pp. 3645-3655 ◽  
Author(s):  
Man-Young Jung ◽  
Soo-Je Park ◽  
So-Jeong Kim ◽  
Jong-Geol Kim ◽  
Jaap S. Sinninghe Damsté ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Ammonia Oxidation ◽  
Soil Horizon ◽  
Ammonia Oxidizer ◽  
Rrna Gene ◽  
Soil Nitrification ◽  
Content Type ◽  
Niche Adaptation ◽  
Group I ◽  
Terrestrial Environments

ABSTRACTSoil nitrification plays an important role in the reduction of soil fertility and in nitrate enrichment of groundwater. Various ammonia-oxidizing archaea (AOA) are considered to be members of the pool of ammonia-oxidizing microorganisms in soil. This study reports the discovery of a chemolithoautotrophic ammonia oxidizer that belongs to a distinct clade of nonmarine thaumarchaeal group I.1a, which is widespread in terrestrial environments. The archaeal strain MY2 was cultivated from a deep oligotrophic soil horizon. The similarity of the 16S rRNA gene sequence of strain MY2 to those of other cultivated group I.1a thaumarchaeota members, i.e.,Nitrosopumilus maritimusand “CandidatusNitrosoarchaeum koreensis,” is 92.9% for both species. Extensive growth assays showed that strain MY2 is chemolithoautotrophic, mesophilic (optimum temperature, 30°C), and neutrophilic (optimum pH, 7 to 7.5). The accumulation of nitrite above 1 mM inhibited ammonia oxidation, while ammonia oxidation itself was not inhibited in the presence of up to 5 mM ammonia. The genome size of strain MY2 was 1.76 Mb, similar to those ofN. maritimusand “Ca. Nitrosoarchaeum koreensis,” and the repertoire of genes required for ammonia oxidation and carbon fixation in thaumarchaeal group I.1a was conserved. A high level of representation of conserved orthologous genes for signal transduction and motility in the noncore genome might be implicated in niche adaptation by strain MY2. On the basis of phenotypic, phylogenetic, and genomic characteristics, we propose the name “CandidatusNitrosotenuis chungbukensis” for the ammonia-oxidizing archaeal strain MY2.

scholarly journals Draft Genome Sequence of Acidobacteria Group 1 Acidipila sp. Strain EB88, Isolated from Forest Soil

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Luiz A. Domeignoz-Horta ◽  
Kristen M. DeAngelis ◽  
Grace Pold
Keyword(s):  
Forest Soil ◽  
Genome Sequence ◽  
Temperate Forest ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Group I ◽  
Group 1

Here, we present the genome sequence of a member of the group I Acidobacteria, Acidipila sp. strain EB88, which was isolated from temperate forest soil.

scholarly journals Abundance and Composition of Epiphytic Bacterial and Archaeal Ammonia Oxidizers of Marine Red and Brown Macroalgae

2011 ◽  
Vol 78 (2) ◽  
pp. 318-325 ◽  
Author(s):  
Rosalia Trias ◽  
Arantzazu García-Lledó ◽  
Noemí Sánchez ◽  
José Luis López-Jurado ◽  
Sara Hallin ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Algal Species ◽  
Western Mediterranean ◽  
Marine Macroalgae ◽  
Ammonia Oxidizing Bacteria ◽  
Marine Environments ◽  
Brown Macroalgae ◽  
Content Type ◽  
Western Mediterranean Sea ◽  
Species Specific

ABSTRACTAmmonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae's potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities on three species of macroalgae,Osmundaria volubilis,Phyllophora crispa, andLaminaria rodriguezii, from the Balearic Islands (western Mediterranean Sea). Quantitative PCR of bacterial and archaeal 16S rRNA andamoAgenes was performed. In contrast to what has been shown for most other marine environments, the macroalgae's surfaces were dominated by bacterialamoAgenes rather than those from the archaeal counterpart. On the basis of the sequences retrieved from AOB and AOAamoAgene clone libraries from each algal species, the bacterial ammonia-oxidizing communities were related toNitrosospiraspp. and toNitrosomonas europaeaand only 6 out of 15 operational taxonomic units (OTUs) were specific for the host species. Conversely, the AOA diversity was higher (43 OTUs) and algal species specific, with 17 OTUs specific forL. rodriguezii, 3 forO. volubilis, and 9 forP. crispa. Altogether, the results suggest that marine macroalgae may exert an ecological niche for AOB in marine environments, potentially through specific microbe-host interactions.

scholarly journals Inhibitory Effects of C2to C101-Alkynes on Ammonia Oxidation in Two Nitrososphaera Species

2015 ◽  
Vol 81 (6) ◽  
pp. 1942-1948 ◽  
Author(s):  
A. E. Taylor ◽  
K. Taylor ◽  
B. Tennigkeit ◽  
M. Palatinszky ◽  
M. Stieglmeier ◽  
...  
Keyword(s):  
Pure Culture ◽  
Ammonia Oxidation ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Monooxygenase ◽  
Inhibitory Effects ◽  
Content Type ◽  
Nitrite Production ◽  
Highly Sensitive ◽  
Production Activity ◽  
Ammonia Oxidizing Bacterium

ABSTRACTA previous study showed that ammonia oxidation by theThaumarchaeotaNitrosopumilus maritimus(group 1.1a) was resistant to concentrations of the C81-alkyne, octyne, which completely inhibits activity by ammonia-oxidizing bacteria. In this study, the inhibitory effects of octyne and other C2to C101-alkynes were evaluated on the nitrite production activity of two pure culture isolates fromThaumarchaeotagroup 1.1b,Nitrososphaera viennensisstrain EN76 andNitrososphaera gargensis. BothN. viennensisandN. gargensiswere insensitive to concentrations of octyne that cause complete and irreversible inactivation of nitrite production by ammonia-oxidizing bacteria. However, octyne concentrations (≥20 μM) that did not inhibitN. maritimuspartially inhibited nitrite production inN. viennensisandN. gargensisin a manner that did not show the characteristics of irreversible inactivation. In contrast to previous studies with an ammonia-oxidizing bacterium,Nitrosomonas europaea, octyne inhibition ofN. viennensiswas: (i) fully and immediately reversible, (ii) not competitive with NH4+, and (iii) without effect on the competitive interaction between NH4+and acetylene. BothN. viennensisandN. gargensisdemonstrated the same overall trend in regard to 1-alkyne inhibition as previously observed forN. maritimus, being highly sensitive to ≤C5alkynes and more resistant to longer-chain length alkynes. Reproducible differences were observed amongN. maritimus,N. viennensis, andN. gargensisin regard to the extent of their resistance/sensitivity to C6and C71-alkynes, which may indicate differences in the ammonia monooxygenase binding and catalytic site(s) among theThaumarchaeota.

scholarly journals Draft Genome Sequence of Urease-Producing Pseudorhodobacter sp. Strain E13, Isolated from the Yellow Sea in Gunsan, South Korea

2019 ◽  
Vol 8 (23) ◽  
Author(s):  
Si Chul Kim ◽  
Hyo Jung Lee
Keyword(s):  
South Korea ◽  
Genome Sequence ◽  
Yellow Sea ◽  
Draft Genome ◽  
The Yellow Sea ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Gram Negative ◽  
Content Type

Here, we report the draft genome sequence of Pseudorhodobacter sp. strain E13, a Gram-negative, aerobic, nonflagellated, and rod-shaped bacterium which was isolated from the Yellow Sea in South Korea. The assembled genome sequence is 3,878,578 bp long with 3,646 protein-coding sequences in 159 contigs.

scholarly journals Complete Genome Sequence of Malassezia restricta CBS 7877, an Opportunist Pathogen Involved in Dandruff and Seborrheic Dermatitis

2019 ◽  
Vol 8 (6) ◽  
Author(s):  
Stanislas C. Morand ◽  
Morgane Bertignac ◽  
Agnes Iltis ◽  
Iris C. R. M. Kolder ◽  
Walter Pirovano ◽  
...  
Keyword(s):  
Human Skin ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Seborrheic Dermatitis ◽  
Skin Microbiome ◽  
Basidiomycetous Yeasts ◽  
Content Type ◽  
Opportunist Pathogen ◽  
Malassezia Restricta

Malassezia restricta, one of the predominant basidiomycetous yeasts present on human skin, is involved in scalp disorders. Here, we report the complete genome sequence of the lipophilic Malassezia restricta CBS 7877 strain, which will facilitate the study of the mechanisms underlying its commensal and pathogenic roles within the skin microbiome.

scholarly journals Complete Genome Sequence of Cupriavidus necator H16 (DSM 428)

2019 ◽  
Vol 8 (37) ◽  
Author(s):  
Gareth T. Little ◽  
Muhammad Ehsaan ◽  
Christian Arenas-López ◽  
Kamran Jawed ◽  
Klaus Winzer ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cupriavidus Necator ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Cupriavidus Necator H16

The hydrogen-utilizing strain Cupriavidus necator H16 (DSM 428) was sequenced using a combination of PacBio and Illumina sequencing. Annotation of this strain reveals 6,543 protein-coding genes, 263 pseudogenes, 64 tRNA genes, and 15 rRNA genes.

scholarly journals Complete Genome Sequence of Stenotrophomonas Phage Mendera

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Kameron D. Garza ◽  
Heather Newkirk ◽  
Russell Moreland ◽  
Carlos F. Gonzalez ◽  
Mei Liu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Stenotrophomonas Maltophilia ◽  
Human Pathogen ◽  
Base Pairs ◽  
Content Type ◽  
Genomic Annotation ◽  
Opportunistic Human Pathogen

Stenotrophomonas maltophilia is an emerging opportunistic human pathogen. In this report, we describe the isolation and genomic annotation of the S. maltophilia-infecting bacteriophage Mendera. A myophage of 159,961 base pairs, Mendera is T4-like and related most closely to Stenotrophomonas phage IME-SM1.

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