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Scientific Reports Jan 2021The modern nitrogen cycle consists of a web of microbially mediated redox transformations. Among the most crucial reactions in this cycle is the oxidation of ammonia to...
The modern nitrogen cycle consists of a web of microbially mediated redox transformations. Among the most crucial reactions in this cycle is the oxidation of ammonia to nitrite, an obligately aerobic process performed by a limited number of lineages of bacteria (AOB) and archaea (AOA). As this process has an absolute requirement for O, the timing of its evolution-especially as it relates to the Great Oxygenation Event ~ 2.3 billion years ago-remains contested and is pivotal to our understanding of nutrient cycles. To estimate the antiquity of bacterial ammonia oxidation, we performed phylogenetic and molecular clock analyses of AOB. Surprisingly, bacterial ammonia oxidation appears quite young, with crown group clades having originated during Neoproterozoic time (or later) with major radiations occurring during Paleozoic time. These results place the evolution of AOB broadly coincident with the pervasive oxygenation of the deep ocean. The late evolution AOB challenges earlier interpretations of the ancient nitrogen isotope record, predicts a more substantial role for AOA during Precambrian time, and may have implications for understanding of the size and structure of the biogeochemical nitrogen cycle through geologic time.
Topics: Ammonium Compounds; Bacteria; Oxidation-Reduction; Phylogeny
PubMed: 33483596
DOI: 10.1038/s41598-021-81718-2 -
Environmental Microbiology May 2022Bacteria in the order 'Candidatus Brocadiales' within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation...
Bacteria in the order 'Candidatus Brocadiales' within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation (anammox). Two families of anammox bacteria with different biogeographical distributions have been reported, marine Ca. Scalinduaceae and freshwater Ca. Brocadiaceae. Here we report evidence of three new species within a novel genus and family of anammox bacteria, which were discovered in biofilms of a subsea road tunnel under a fjord in Norway. In this particular ecosystem, the nitrogen cycle is likely fuelled by ammonia from organic matter degradation in the fjord sediments and the rock mass above the tunnel, resulting in the growth of biofilms where anammox bacteria can thrive under oxygen limitation. We resolved several metagenome-assembled genomes (MAGs) of anammox bacteria, including three Ca. Brocadiales MAGs that could not be classified at the family level. MAGs of this novel family had all the diagnostic genes for a full anaerobic ammonium oxidation pathway in which nitrite was probably reduced by a NirK-like reductase. A survey of published molecular data indicated that this new family of anammox bacteria occurs in many marine sediments, where its members presumably would contribute to nitrogen loss.
Topics: Ammonium Compounds; Anaerobic Ammonia Oxidation; Anaerobiosis; Bacteria; Bacteria, Anaerobic; Ecosystem; Metagenome; Oxidation-Reduction
PubMed: 35415863
DOI: 10.1111/1462-2920.16006 -
Plant Signaling & Behavior Feb 2013Plastid retrograde signaling (chloroplast to nucleus) has been proposed to play an important role in the acclimation of plant function to environmental stress. Although... (Review)
Review
Plastid retrograde signaling (chloroplast to nucleus) has been proposed to play an important role in the acclimation of plant function to environmental stress. Although several pathways and molecular components, as well as some signals, have been identified in recent years, our understanding of the communication between plastid and nucleus under stress remains fragmentary. This mini-review summarizes the properties of currently proposed candidate signals, chief molecular components, and their roles in the plastid retrograde signaling network in a variety of stress responses. We provide special emphasis on the recently characterized AMOS1/EGY1-dependent plastid retrograde signaling pathways engaged during ammonium stress.
Topics: Ammonium Compounds; Gene Expression Regulation, Plant; Plant Proteins; Plastids; Signal Transduction
PubMed: 23299427
DOI: 10.4161/psb.23107 -
Microbes and Environments 2022Anaerobic ammonium-oxidizing (anammox) bacteria are slow-growing and fastidious bacteria, and limited numbers of enrichment cultures have been established. A metagenomic...
Anaerobic ammonium-oxidizing (anammox) bacteria are slow-growing and fastidious bacteria, and limited numbers of enrichment cultures have been established. A metagenomic ana-lysis of our 5 established anammox bacterial enrichment cultures was performed in the present study. Fourteen high-quality metagenome-assembled genomes (MAGs) were obtained, including those of 5 anammox Planctomycetota (Candidatus Brocadia, Ca. Kuenenia, Ca. Jettenia, and Ca. Scalindua), 4 Bacteroidota, and 3 Chloroflexota. Based on the gene sets of metabolic pathways involved in the degradation of polymeric substances found in Chloroflexota and Bacteroidota MAGs, they are expected to be scavengers of extracellular polymeric substances and cell debris.
Topics: Ammonium Compounds; Anaerobic Ammonia Oxidation; Anaerobiosis; Bacteria; Metagenome; Metagenomics; Oxidation-Reduction; RNA, Ribosomal, 16S
PubMed: 35811137
DOI: 10.1264/jsme2.ME22017 -
Microbial Ecology Aug 2020The aim of this study was isolation and characterization of heterotrophic bacteria capable of ammonium and nitrite removal at 15 °C (optimal temperature for growing...
The aim of this study was isolation and characterization of heterotrophic bacteria capable of ammonium and nitrite removal at 15 °C (optimal temperature for growing rainbow trout Oncorhynchus mykiss). Environmental isolates were grown in liquid media containing ammonium or nitrite, and best strains in terms of growth and ammonium or nitrite removal were identified via 16S rRNA sequencing. Dyadobacter sp. (no. 68) and Janthinobacterium sp. (no. 100) were selected for optimal adaptation to growth at 15 °C and best ammonium and nitrite removal (P < 0.05), respectively. A heterotrophic ammonium and nitrite removal (HAN) microbial complex, containing selected strains, was prepared and applied in a trout culture system. After 10 days, the effect of microbial HAN complex was investigated in terms of ammonium and nitrite removal, as well as stress and immune indices present in the plasma of cultivated trout. Compared to a standard cultivation setup, addition of the HAN complex had a clear beneficial effect on keeping the un-ionized ammonia and nitrite level below prescribed standards (P < 0.05). This resulted in reduction of stress and immune reactions of cultivated fish (P < 0.05), leading to an augmentation of final weight and survival. Application of the selected microbial complex resulted in a significant improvement of the aquaculture ecosystem.
Topics: Ammonium Compounds; Animals; Aquaculture; Bacteria; Heterotrophic Processes; Nitrites; Oncorhynchus mykiss
PubMed: 32162039
DOI: 10.1007/s00248-020-01498-6 -
Molecular Biology and Evolution Aug 2022The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of...
The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of the global nitrogen loss in surface environments. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remain enigmatic. Here, we performed a comprehensive phylogenomic and molecular clock analysis of anammox bacteria within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates, which include implementing both a traditional cyanobacteria-based and a recently developed mitochondria-based molecular dating approach, we estimated a consistent origin of anammox bacteria at early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32-2.5 Ga) which fundamentally changed global biogeochemical cycles. We further showed that during the origin of anammox bacteria, genes involved in oxidative stress adaptation, bioenergetics, and anammox granules formation were recruited, which might have contributed to their survival on an increasingly oxic Earth. Our findings suggest the rising levels of atmospheric oxygen, which made nitrite increasingly available, was a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link the GOE to the evolution of obligate anaerobic bacteria.
Topics: Ammonium Compounds; Anaerobic Ammonia Oxidation; Anaerobiosis; Bacteria; Bacteria, Anaerobic; Nitrites; Nitrogen; Oxidation-Reduction; Phylogeny; Quaternary Ammonium Compounds
PubMed: 35920138
DOI: 10.1093/molbev/msac170 -
International Journal of Environmental... Aug 2020Tannery sludge usually has high content of trivalent chromium (Cr(III)) and ammonium-nitrogen (NH-N). It is important to make a critical evaluation of the releasing...
Tannery sludge usually has high content of trivalent chromium (Cr(III)) and ammonium-nitrogen (NH-N). It is important to make a critical evaluation of the releasing behaviors of Cr(III) and NH-N from tannery sludge before its use on improving soil fertility in agricultural applications. For this purpose, static batch and dynamic leaching experiments with different mathematical models were carried out to simulate the Cr(III) and NH-N releasing kinetics from tannery sludge sampled in a typical tannery disposal site in North China, and their influencing factors were also discussed. The results showed that a larger solid-liquid ratio, a higher temperature, and a lower pH value of the leaching solution were beneficial for the release of Cr(III) and NH-N from the tannery sludge. The release kinetics of Cr(III) and NH-N followed parabolic diffusion and simple Elovich models both in the static and dynamic leaching conditions, indicating that the release was a complex heterogeneous diffusion process. The NH-N was easy to be leached out and its released amount reached 3.14 mg/g under the dynamic leaching condition (pH 7), whereas the released amount of the Cr(III) was only 0.27 μg/g from the tannery sludge. There was a positive correlation coefficient between dissolved Fe and Cr(III) in the leachate under different leaching conditions, and the calculated average ratio of Fe/Cr(III) concentration was 3.56, indicating that the small amount of the released Cr(III) came from the dissolution of CrFe(OH) minerals in tannery sludge.
Topics: Ammonium Compounds; China; Chromium; Industrial Waste; Nitrogen; Sewage; Tanning
PubMed: 32824851
DOI: 10.3390/ijerph17166003 -
Molecules (Basel, Switzerland) Mar 2020An innovative automatic purge-and-trap (P&T) system coupled with fluorimetric sequential injection (SI), for the on-line separation and preconcentration of volatile...
An innovative automatic purge-and-trap (P&T) system coupled with fluorimetric sequential injection (SI), for the on-line separation and preconcentration of volatile compounds, is presented. The truth of concept is demonstrated for the ammonium fluorimetric determination in environmental water samples with complex matrices without any pretreatment. The P&T flow system comprises a thermostated purge-vessel where ammonium is converted into gaseous ammonia and a trap-vessel for ammonia collection. This configuration results in matrix removal as well as analyte preconcentration, avoiding membrane-associated problems. All the main parameters affecting the efficiency of a P&T system were studied and optimized. The proposed method is characterized by a working range of 2.7-150.0 μg L of NH, with a detection and quantification limit of 0.80 and 2.66 μg L, respectively, for a 10-mL sample consumption. The accuracy of the method was assessed by recovery assays in seawater, estuarine, and lake water samples as well as by the analysis of standard reference material.
Topics: Ammonium Compounds; Estuaries; Flow Injection Analysis; Fluorometry; Gases; Hydrochloric Acid; Hydrogen-Ion Concentration; Limit of Detection; Seawater; Temperature; Water Pollutants, Chemical
PubMed: 32235335
DOI: 10.3390/molecules25071569 -
Current Biology : CB Dec 2022Increasing nitrogen (N) deposition often tends to negatively impact the functions of belowground ectomycorrhizal networks, although the exact molecular mechanisms...
Increasing nitrogen (N) deposition often tends to negatively impact the functions of belowground ectomycorrhizal networks, although the exact molecular mechanisms underlying this trait are still unclear. Here, we assess how the root-associated fungus Clitopilus hobsonii establishes an ectomycorrhiza-like association with its host tree Populus tomentosa and how this interaction is favored by organic N over mineral N. The establishment of a functional symbiosis in the presence of organic N promotes plant growth and the transfer of N from the fungus to above ground plant tissues. Genomic traits and in planta transcriptional signatures suggest that C. hobsonii may have a dual lifestyle with saprotrophic and mutualistic traits. For example, several genes involved in the digestion of cellulose and hemicellulose are highly expressed during the interaction, whereas the expression of multiple copies of pectin-digesting genes is tightly controlled. Conversely, the nutritional mutualism is dampened in the presence of ammonium (NH) or nitrate (NO). Increasing levels of NH led to a higher expression of pectin-digesting genes and a continuous increase in hydrogen peroxide production in roots, whereas the presence of NO resulted in toxin production. In summary, our results suggest that C. hobsonii is a facultative ectomycorrhizal fungus. Access to various forms of N acts as an on/off switch for mutualism caused by large-scale fungal physiological remodeling. Furthermore, the abundance of pectin-degrading enzymes with distinct expression patterns during functional divergence after exposure to NH or organic N is likely to be central to the transition from parasitism to mutualism.
Topics: Mycorrhizae; Nitrogen; Symbiosis; Nitrates; Ammonium Compounds; Plant Roots
PubMed: 36402137
DOI: 10.1016/j.cub.2022.10.054 -
Journal of Bacteriology Jul 1954
Topics: Ammonium Compounds; Animals; Bacillus; Insecta; Oxidoreductases
PubMed: 13183914
DOI: 10.1128/jb.68.1.129-130.1954