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 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 Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations

2013 ◽  
Vol 79 (22) ◽  
pp. 6911-6916 ◽  
Author(s):  
Tatsunori Nakagawa ◽  
David A. Stahl
Keyword(s):  
Ammonia Oxidation ◽  
Physiological State ◽  
Transcriptional Response ◽  
Ammonia Oxidizer ◽  
Mrna Levels ◽  
Marine Microorganisms ◽  
Transcript Levels ◽  
Content Type ◽  
Ammonia Oxidizing Archaea ◽  
Ammonia Transport

ABSTRACTThe ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO2fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeonNitrosopumilus maritimusSCM1 growing at two ammonia concentrations, as measured by combined ammonia and ammonium, one well above theKmfor ammonia oxidation (∼500 μM) and the other well below theKm(<10 nM). Transcript levels were generally immediately and differentially repressed when cells transitioned from ammonia-replete to ammonia-limiting conditions. Transcript levels for ammonia oxidation, CO2fixation, and one of the ammonia transport genes were approximately the same at high and low ammonia availability. Transcripts for all analyzed genes decreased with time in the complete absence of ammonia, but with various rates of decay. The new steady-state mRNA levels established are presumably more reflective of the natural physiological state of ammonia-oxidizing archaea and offer a reference for interpreting message abundance patterns in the natural environment.

scholarly journals Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

2013 ◽  
Vol 79 (13) ◽  
pp. 3974-3985 ◽  
Author(s):  
Barbara J. MacGregor ◽  
Jennifer F. Biddle ◽  
Andreas Teske
Keyword(s):  
Gulf Of California ◽  
Bacterial Species ◽  
Draft Genome ◽  
Genetic Exchange ◽  
23S Rrna ◽  
Rrna Gene ◽  
Homing Endonucleases ◽  
Guaymas Basin ◽  
Content Type ◽  
Group I

ABSTRACTThe draft genome sequence of a single orangeBeggiatoa(“CandidatusMaribeggiatoa”) filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to thefdxNexcision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non-Beggiatoaceaematches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in otherBeggiatoaceaegenomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.

scholarly journals Thaumarchaeal Ammonia Oxidation in an Acidic Forest Peat Soil Is Not Influenced by Ammonium Amendment

2010 ◽  
Vol 76 (22) ◽  
pp. 7626-7634 ◽  
Author(s):  
Nejc Stopnišek ◽  
Cécile Gubry-Rangin ◽  
Špela Höfferle ◽  
Graeme W. Nicol ◽  
Ines Mandič-Mulec ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Inorganic Nitrogen ◽  
Peat Soil ◽  
Selective Advantage ◽  
Ammonia Oxidizer ◽  
Ammonium Concentration ◽  
Rrna Gene ◽  
Ammonia Oxidizers ◽  
Ammonia Release

ABSTRACT Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and “deep peat” lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.

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 Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth

mBio ◽  
2019 ◽  
Vol 10 (3) ◽  
Author(s):  
Kelley Hurst-Hess ◽  
Rajesh Biswas ◽  
Yong Yang ◽  
Paulami Rudra ◽  
Erica Lasek-Nesselquist ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Exponential Growth ◽  
Sigma Factor ◽  
Housekeeping Genes ◽  
Sigma Factors ◽  
Rrna Gene ◽  
Content Type ◽  
Group I ◽  
Group Ii

ABSTRACTMycobacterial σBbelongs to the group II family of sigma factors, which are widely considered to transcribe genes required for stationary-phase survival and the response to stress. Here we explored the mechanism underlying the observed hypersensitivity of ΔsigBdeletion mutants ofMycobacteriumsmegmatis,M. abscessus, andM. tuberculosisto rifampin (RIF) and uncovered an additional constitutive role of σBduring exponential growth of mycobacteria that complements the function of the primary sigma factor, σA. Using chromatin immunoprecipitation sequencing (ChIP-Seq), we show that during exponential phase, σBbinds to over 200 promoter regions, including those driving expression of essential housekeeping genes, like the rRNA gene. ChIP-Seq of ectopically expressed σA-FLAG demonstrated that at least 61 promoter sites are recognized by both σAand σB. These results together suggest that RNA polymerase holoenzymes containing either σAor σBtranscribe housekeeping genes in exponentially growing mycobacteria. The RIF sensitivity of the ΔsigBmutant possibly reflects a decrease in the effective housekeeping holoenzyme pool, which results in susceptibility of the mutant to lower doses of RIF. Consistent with this model, overexpression of σArestores the RIF tolerance of the ΔsigBmutant to that of the wild type, concomitantly ruling out a specialized role of σBin RIF tolerance. Although the properties of mycobacterial σBparallel those ofEscherichiacoliσ38in its ability to transcribe a subset of housekeeping genes, σBpresents a clear departure from theE. coliparadigm, wherein the cellular levels of σ38are tightly controlled during exponential growth, such that the transcription of housekeeping genes is initiated exclusively by a holoenzyme containing σ70(E.σ70).IMPORTANCEAll mycobacteria encode a group II sigma factor, σB, closely related to the group I principal housekeeping sigma factor, σA. Group II sigma factors are widely believed to play specialized roles in the general stress response and stationary-phase transition in the bacteria that encode them. Contrary to this widely accepted view, we show an additional housekeeping function of σBthat complements the function of σAin logarithmically growing cells. These findings implicate a novel and dynamic partnership between σAand σBin maintaining the expression of housekeeping genes in mycobacteria and can perhaps be extended to other bacterial species that possess multiple group II sigma factors.

scholarly journals The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes

2020 ◽  
Vol 11 ◽  
Author(s):  
João Pereira Santos ◽  
António G. G. Sousa ◽  
Hugo Ribeiro ◽  
Catarina Magalhães
Keyword(s):  
Ammonia Oxidation ◽  
Estuarine Sediments ◽  
Ammonia Oxidizer ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Salinity Regime ◽  
Salinity Fluctuation ◽  
Ammonia Oxidizing Archaea ◽  
Negative Effect ◽  
The Impact

Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.

scholarly journals Phenotypic and Phylogenetic Identification of Coliform Bacteria Obtained Using 12 Coliform Methods Approved by the U.S. Environmental Protection Agency

2015 ◽  
Vol 81 (17) ◽  
pp. 6012-6023 ◽  
Author(s):  
Ya Zhang ◽  
Pei-Ying Hong ◽  
Mark W. LeChevallier ◽  
Wen-Tso Liu
Keyword(s):  
16S Rrna ◽  
Environmental Protection ◽  
Environmental Protection Agency ◽  
Coliform Bacteria ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Growth Responses ◽  
Protection Agency ◽  
Content Type ◽  
Group I

ABSTRACTThe current definition of coliform bacteria is method dependent, and when different culture-based methods are used, discrepancies in results can occur and affect the accuracy of identification of true coliforms. This study used an alternative approach to the identification of true coliforms by combining the phenotypic traits of the coliform isolates and the phylogenetic affiliation of 16S rRNA gene sequences with the use oflacZanduidAgenes. A collection of 1,404 isolates detected by 12 U.S. Environmental Protection Agency-approved coliform-testing methods were characterized based on their phylogenetic affiliations and responses to their original isolation media and lauryl tryptose broth, m-Endo, and MI agar media. Isolates were phylogenetically classified into 32 true-coliform, or targetedEnterobacteriaceae(TE), groups and 14 noncoliform, or nontargetedEnterobacteriaceae(NTE), groups. It was shown statistically that detecting true-positive (TP) events is more challenging than detecting true-negative (TN) events. Furthermore, most false-negative (FN) events were associated with four TE groups (i.e.,Serratiagroup I and theProvidencia,Proteus, andMorganellagroups) and most false-positive (FP) events with two NTE groups, theAeromonasandPlesiomonasgroups. InEscherichia colitesting, 18 out of 145E. coliisolates identified by enzymatic methods were validated as FN. The reasons behind the FP and FN reactions could be explained through analysis of thelacZanduidAgenes. Overall, combining the analyses of the 16S rRNA,lacZ, anduidAgenes with the growth responses of TE and NTE on culture-based media is an effective way to evaluate the performance of coliform detection methods.

scholarly journals Microbial community analysis of biofilters reveals a dominance of either comammox Nitrospira or archaea as ammonia oxidizers in freshwater aquaria

2021 ◽  
Author(s):  
Michelle M McKnight ◽  
Josh D Neufeld
Keyword(s):  
Microbial Communities ◽  
Ammonia Oxidation ◽  
16S Rrna Gene Sequencing ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Ammonia Oxidizer ◽  
Future Research ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers

Nitrification by aquarium biofilters transforms toxic ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Ammonia oxidation is mediated by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizing (comammox) Nitrospira. Prior to the discovery of comammox Nitrospira, previous research revealed that AOA dominate among ammonia oxidizers in freshwater biofilters. Here, we characterized the composition of aquarium filter microbial communities and quantified the abundance of all three known groups of ammonia oxidizers. Aquarium biofilter and water samples were collected from representative freshwater and saltwater systems in Southwestern Ontario, Canada. Using extracted DNA, we performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to assess community composition and quantify the abundance of amoA genes, respectively. Our results show that aquarium biofilter microbial communities were consistently represented by putative heterotrophs of the Proteobacteria and Bacteroides phyla, with distinct profiles associated with fresh versus saltwater biofilters. Among nitrifiers, comammox Nitrospira amoA genes were detected in all 38 freshwater aquarium biofilter samples and were the most abundant ammonia oxidizer in 30 of these samples, with the remaining biofilters dominated by AOA, based on amoA gene abundances. In saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. These results demonstrate that comammox Nitrospira play an important role in biofilter nitrification that has been previously overlooked and such microcosms are useful for exploring the ecology of nitrification for future research.

scholarly journals Magnetospira thiophila gen. nov., sp. nov., a marine magnetotactic bacterium that represents a novel lineage within the Rhodospirillaceae ( Alphaproteobacteria )

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2443-2450 ◽  
Author(s):  
Timothy J. Williams ◽  
Christopher T. Lefèvre ◽  
Weidong Zhao ◽  
Terry J. Beveridge ◽  
Dennis A. Bazylinski
Keyword(s):  
Carbon Fixation ◽  
Lima Bean ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Magnetotactic Bacterium ◽  
Single Chain ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Semi Solid

A marine, magnetotactic bacterium, designated strain MMS-1T, was isolated from mud and water from a salt marsh in Woods Hole, Massachusetts, USA, after enrichment in defined oxygen-concentration/redox-gradient medium. Strain MMS-1T is an obligate microaerophile capable of chemoorganoheterotrophic and chemolithoautotrophic growth. Optimal growth occurred at pH 7.0 and 24–26 °C. Chemolithoautotrophic growth occurred with thiosulfate as the electron donor and autotrophic carbon fixation was via the Calvin–Benson–Bassham cycle. The G+C content of the DNA of strain MMS-1T was 47.2 mol%. Cells were Gram-negative and morphologically variable, with shapes that ranged from that of a lima bean to fully helical. Cells were motile by means of a single flagellum at each end of the cell (amphitrichous). Regardless of whether grown in liquid or semi-solid cultures, strain MMS-1T displayed only polar magnetotaxis and possessed a single chain of magnetosomes containing elongated octahedral crystals of magnetite, positioned along the long axis of the cell. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS-1T belongs to the family Rhodospirillaceae within the Alphaproteobacteria , and is distantly related to species of the genus Magnetospirillum . Strain MMS-1T is therefore considered to represent a novel species of a new genus, for which the name Magnetospira thiophila gen. nov., sp. nov. is proposed. The type strain of Magnetospira thiophila is MMS-1T ( = ATCC BAA-1438T = JCM 17960T).

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