scholarly journals Cultivation of Autotrophic Ammonia-Oxidizing Archaea from Marine Sediments in Coculture with Sulfur-Oxidizing Bacteria

2010 ◽  
Vol 76 (22) ◽  
pp. 7575-7587 ◽  
Author(s):  
Byoung-Joon Park ◽  
Soo-Je Park ◽  
Dae-No Yoon ◽  
Stefan Schouten ◽  
Jaap S. Sinninghe Damsté ◽  
...  
Keyword(s):  
16S Rrna ◽  
Marine Sediments ◽  
Ammonia Oxidation ◽  
Enrichment Culture ◽  
Gene Copy ◽  
Initial Growth ◽  
Ammonia Oxidizing Archaea ◽  
Group I ◽  
Sulfur Oxidizing ◽  
Sulfur Oxidizing Bacteria

ABSTRACT The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and “Candidatus Nitrosopumilus maritimus” (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichment of AOA over ammonia-oxidizing bacteria (AOB) is likely due to the reduced oxygen levels caused by the rapid initial growth of SOB. After biweekly transfers for ca. 20 months, archaeal cells became the dominant prokaryotes (>80%), based on quantitative PCR and fluorescence in situ hybridization analysis. The increase of archaeal 16S rRNA gene copy numbers was coincident with the amount of ammonia oxidized, and expression of the archaeal amoA gene was observed during ammonia oxidation. Bacterial amoA genes were not detected in the enrichment culture. The affinities of these AOA to oxygen and ammonia were substantially higher than those of AOB. [13C]bicarbonate incorporation and the presence and activation of genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle indicated autotrophy during ammonia oxidation. In the enrichment culture, ammonium was oxidized to nitrite by the AOA and subsequently to nitrate by Nitrospina-like bacteria. Our experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments.

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.

Diversity of Culturable Bacteria in an Alkaliphilic Sulfur-Oxidizing Microbial Consortium

2009 ◽  
Vol 71-73 ◽  
pp. 137-140 ◽  
Author(s):  
C. Granada ◽  
S. Revah ◽  
Sylvie Le Borgne
Keyword(s):  
16S Rrna ◽  
Microbial Consortium ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
Group I ◽  
Colonial Morphology ◽  
Sulfur Oxidizing ◽  
Sulfur Oxidizing Bacteria

Alkaliphilic sulfur-oxidizing bacteria were isolated from an alkaliphilic microbial consortium used to treat H2S at pH>9 in a laboratory scale biofilter. Nineteen isolates were obtained. These isolates could be grouped based on their colonial morphology on a solid medium containing thiosulfate as sole energy source. Half of the isolates presented yellow colonies (group I). This yellowish colonial morphology is typically found in the genus Thioalkalivibrio. For the rest of the isolates, the colonies were white (group II) or transparent (group III). The isolates of each group were characterized by ribosomal intergenic spacer analysis and restriction analysis of their 16S rRNA genes. One of the yellow isolates presented 85% of homology with Thioalkalivibrio jannaschii by partial sequencing of its 16S rRNA gene. The genus Thioalkalivibrio comprises extremely haloalkaliphilic sulfur-oxidizing bacteria that have been proposed as suitable biocatalysts for natural gas desulfurization.

scholarly journals Core and Intact Polar Glycerol Dibiphytanyl Glycerol Tetraether Lipids of Ammonia-Oxidizing Archaea Enriched from Marine and Estuarine Sediments

2011 ◽  
Vol 77 (10) ◽  
pp. 3468-3477 ◽  
Author(s):  
Angela Pitcher ◽  
Ellen C. Hopmans ◽  
Annika C. Mosier ◽  
Soo-Je Park ◽  
Sung-Keun Rhee ◽  
...  
Keyword(s):  
San Francisco ◽  
Marine Sediments ◽  
Membrane Lipids ◽  
Hot Spring ◽  
Enrichment Culture ◽  
Estuarine Sediments ◽  
Content Type ◽  
Ammonia Oxidizing Archaea ◽  
Coastal Marine ◽  
Group I

ABSTRACTGlycerol dibiphytanyl glycerol tetraether (GDGT)-based intact membrane lipids are increasingly being used as complements to conventional molecular methods in ecological studies of ammonia-oxidizing archaea (AOA) in the marine environment. However, the few studies that have been done on the detailed lipid structures synthesized by AOA in (enrichment) culture are based on species enriched from nonmarine environments, i.e., a hot spring, an aquarium filter, and a sponge. Here we have analyzed core and intact polar lipid (IPL)-GDGTs synthesized by three newly available AOA enriched directly from marine sediments taken from the San Francisco Bay estuary (“CandidatusNitrosoarchaeum limnia”), and coastal marine sediments from Svalbard, Norway, and South Korea. Like previously screened AOA, the sedimentary AOA all synthesize crenarchaeol (a GDGT containing a cyclohexane moiety and four cyclopentane moieties) as a major core GDGT, thereby supporting the hypothesis that crenarchaeol is a biomarker lipid for AOA. The IPL headgroups synthesized by sedimentary AOA comprised mainly monohexose, dihexose, phosphohexose, and hexose-phosphohexose moieties. The hexose-phosphohexose headgroup bound to crenarchaeol was common to all enrichments and, in fact, the only IPL common to every AOA enrichment analyzed to date. This apparent specificity, in combination with its inferred lability, suggests that it may be the most suitable biomarker lipid to trace living AOA. GDGTs bound to headgroups with a mass of 180 Da of unknown structure appear to be specific to the marine group I.1a AOA: they were synthesized by all three sedimentary AOA and “CandidatusNitrosopumilus maritimus”; however, they were absent in the group I.1b AOA “CandidatusNitrososphaera gargensis.”

scholarly journals Soil Amendments Alter Ammonia-Oxidizing Archaea and Bacteria Communities in Rain-Fed Maize Field in Semi-Arid Loess Plateau

Land ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1039
Author(s):  
Setor Kwami Fudjoe ◽  
Lingling Li ◽  
Yuji Jiang ◽  
Benjamin Karikari ◽  
Junhong Xie ◽  
...  
Keyword(s):  
Loess Plateau ◽  
Soil Amendments ◽  
Gene Copy ◽  
Cow Manure ◽  
Urea Fertilizer ◽  
Nitrification Activity ◽  
Ammonia Oxidizing Archaea ◽  
Potential Nitrification ◽  
Group I ◽  
Semi Arid

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are key drivers of nitrification in rainfed soil ecosystems. However, within a semi-arid region, the influence of different soil amendments on the composition of soil AOA and AOB communities and soil properties of rainfed maize is still unclear. Therefore, in this study, the abundance, diversity, and composition of AOA and AOB communities and the potential nitrification activity (PNA) was investigated across five soil treatments: no fertilization (NA), urea fertilizer (CF), cow manure (SM), corn stalk (MS), and cow manure + urea fertilizer (SC). The AOB amoA gene copy number was influenced significantly by fertilization treatments. The AOB community was dominated by Nitrosospira cluster 3b under the CF and SC treatments, and the AOA community was dominated by Nitrososphaera Group I.1b under the CF and NA amendments; however, manure treatments (SM, MS, and SC) did not exhibit such influence. Network analysis revealed the positive impact of some hub taxonomy on the abundance of ammonia oxidizers. Soil pH, NO3−-N, Module 3, biomass, and AOB abundance were the major variables that influenced the potential nitrification activity (PNA) within structural equation modeling. PNA increased by 142.98–226.5% under the treatments CF, SC, SM, and MS compared to NA. In contrast to AOA, AOB contributed dominantly to PNA. Our study highlights the crucial role of bacterial communities in promoting sustainable agricultural production in calcareous soils in semi-arid loess plateau environments.

scholarly journals Ammonia-oxidizing Archaea (AOA) are Winners to Survive in Oxygen-limited Habitat Compared to Ammonia-oxidizing Bacteria (AOB)

2021 ◽  
Author(s):  
Peigang Dai ◽  
Wenjing Song ◽  
Zhao Che ◽  
Lili Zhang ◽  
Zhaorong Dong
Keyword(s):  
Intertidal Zone ◽  
High Throughput Sequencing ◽  
Ammonia Oxidation ◽  
Illumina Miseq ◽  
Gene Copy ◽  
Ammonia Oxidizing Bacteria ◽  
Niche Specialization ◽  
Ammonia Oxidizing Archaea ◽  
Copy Numbers ◽  
Oxidation Reduction

Abstract Purpose: Both ammonia oxidizing archaea (AOA) and bacteria (AOB) perform the ammonia oxidation together. These two kinds of microbes present a convenient model for studying niche specialization. To date, few surveys concentrated on the influence of oxygen concentration on niche specialization of AOA and AOB in intertidal zones. Methods: Here, high-throughput sequencing by Illumina MiSeq and qPCR were applied to detect the change of abundance, diversity as well as community structure of both AOA and AOB with 0-60 cm sediments depth in the intertidal zone in Qingdao.Results and Conclusion: The AOA/AOB amoA gene copy numbers and AOA/AOB OTU numbers were all increased as sediment depth went deeper, which indicated that AOA were more adaptive to oxygen-limited niches compared to AOB and oxygen indeed led to the niche specialization of AOA and AOB in intertidal sediments. The dominant AOA and AOB were the Nitrosopumilus and Nitrosospira clusters, respectively, which indicated an ecological success in intertidal zone. Oxidation-reduction potential (ORP) was significantly positively correlated with AOB abundance and AOB OTU numbers (P < 0.01). In addition, both TN (P < 0.01) and pH (P < 0.05) were significantly and negatively correlated with AOB abundance. TN was also significantly and negatively correlated with AOB OTU numbers (P < 0.05).

scholarly journals Community Structure of Ammonia-Oxidizing Bacteria within Anoxic Marine Sediments

2003 ◽  
Vol 69 (3) ◽  
pp. 1359-1371 ◽  
Author(s):  
Thomas E. Freitag ◽  
James I. Prosser
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
16S Rdna ◽  
Marine Sediments ◽  
Ammonia Oxidation ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizing Bacteria ◽  
Anaerobic Oxidation ◽  
Banding Patterns

ABSTRACT The potential for oxidation of ammonia in anoxic marine sediments exists through anaerobic oxidation by Nitrosomonas-like organisms, utilizing nitrogen dioxide, coupling of nitrification, manganese reduction, and anaerobic oxidation of ammonium by planctomycetes (the Anammox process). Here we describe the presence of microbial communities with the potential to carry out these processes in a natural marine sediment system (Loch Duich, Scotland). Natural microbial communities of Planctomycetales-Verrucomicrobia and β- and γ-proteobacterial ammonia-oxidizing bacteria were characterized by analysis of 16S rRNA genes amplified using group-specific primers by PCR- and reverse transcription-PCR amplification of 16S rDNA and RNA, respectively. Amplification products were analyzed by sequencing of clones and by denaturant gradient gel electrophoresis (DGGE). Amplification of primers specific for Planctomycetales-Verrucomicrobia and β-proteobacterial ammonia-oxidizing bacteria generated products at all sampling sites and depths, but no product was generated using primers specific for γ-proteobacterial ammonia-oxidizing bacteria. 16S rDNA DGGE banding patterns indicated complex communities of β-proteobacterial ammonia-oxidizing bacteria in anoxic marine sediments. Phylogenetic analysis of sequences from clones and those excised from DGGE gels suggests dominance of Nitrosospira cluster 1-like organisms and of strains belonging to a novel cluster represented in dominant bands in 16S rRNA DGGE banding patterns. Their presence indicates a group of organisms closely related to recognized β-proteobacterial ammonia-oxidizing bacteria that may be selected in anoxic environments and may be capable of anoxic ammonia oxidation. Sequence analysis of planctomycete clone libraries and sequences excised from DGGE gels also demonstrated a diverse microbial community and suggested the presence of new subdivisions, but no sequence related to recognized Anammox organisms was detected.

scholarly journals Comparative Analysis of 16S rRNA andamoAGenes from Archaea Selected with Organic and Inorganic Amendments in Enrichment Culture

2012 ◽  
Vol 78 (7) ◽  
pp. 2137-2146 ◽  
Author(s):  
Mouzhong Xu ◽  
Jon Schnorr ◽  
Brandon Keibler ◽  
Holly M. Simon
Keyword(s):  
Comparative Analysis ◽  
16S Rrna ◽  
Ammonia Oxidation ◽  
Organic Amendment ◽  
Enrichment Culture ◽  
Plant Root ◽  
Rrna Gene ◽  
Potential Growth ◽  
Inorganic Amendments ◽  
Coupled Growth

ABSTRACTWe took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA andamoAgenes indicated that specific archaeal clades were selected under different conditions. ThreeamoAsequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the “root” clade, we detected no correspondingamoAgene. TheamoA-containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis ofamoAgene abundance and expression, together with nitrification-coupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, althoughamoA-containing group 1.1a archaea were present in enrichments, we detected neither expression ofamoAgenes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized.

scholarly journals Lipid Biomarkers and Carbon Isotope Signatures of a Microbial (Beggiatoa) Mat Associated with Gas Hydrates in the Gulf of Mexico

2005 ◽  
Vol 71 (4) ◽  
pp. 2106-2112 ◽  
Author(s):  
Chuanlun L. Zhang ◽  
Zhiyong Huang ◽  
James Cantu ◽  
Richard D. Pancost ◽  
Robin L. Brigmon ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Confocal Microscopy ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gulf Of Mexico ◽  
Gas Hydrates ◽  
Lipid Biomarkers ◽  
Rrna Gene ◽  
Sulfur Oxidizing ◽  
Sulfur Oxidizing Bacteria

ABSTRACT White and orange mats are ubiquitous on surface sediments associated with gas hydrates and cold seeps in the Gulf of Mexico. The goal of this study was to determine the predominant pathways for carbon cycling within an orange mat in Green Canyon (GC) block GC 234 in the Gulf of Mexico. Our approach incorporated laser-scanning confocal microscopy, lipid biomarkers, stable carbon isotopes, and 16S rRNA gene sequencing. Confocal microscopy showed the predominance of filamentous microorganisms (4 to 5 μm in diameter) in the mat sample, which are characteristic of Beggiatoa. The phospholipid fatty acids extracted from the mat sample were dominated by 16:1ω7c/t (67%), 18:1ω7c (17%), and 16:0 (8%), which are consistent with lipid profiles of known sulfur-oxidizing bacteria, including Beggiatoa. These results are supported by the 16S rRNA gene analysis of the mat material, which yielded sequences that are all related to the vacuolated sulfur-oxidizing bacteria, including Beggiatoa, Thioploca, and Thiomargarita. The δ13C value of total biomass was −28.6‰; those of individual fatty acids were −29.4 to −33.7‰. These values suggested heterotrophic growth of Beggiatoa on organic substrates that may have δ13C values characteristic of crude oil or on their by-products from microbial degradation. This study demonstrated that integrating lipid biomarkers, stable isotopes, and molecular DNA could enhance our understanding of the metabolic functions of Beggiatoa mats in sulfide-rich marine sediments associated with gas hydrates in the Gulf of Mexico and other locations.

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