scholarly journals Nutrient-Limited Enrichments of Nitrifiers From Soil Yield Consortia of Nitrosocosmicus-Affiliated AOA and Nitrospira-Affiliated NOB

2021 ◽  
Vol 12 ◽  
Author(s):  
Jonathan Rodriguez ◽  
Seemanti Chakrabarti ◽  
Eunkyung Choi ◽  
Nisreen Shehadeh ◽  
Samantha Sierra-Martinez ◽  
...  
Keyword(s):  
Microbial Community Composition ◽  
Gene Sequencing ◽  
Terrestrial Ecosystems ◽  
High Yield ◽  
Growth Media ◽  
Kinetic Properties ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizing Archaea ◽  
Enrichment Strategy

The discovery of ammonia-oxidizing archaea (AOA) and complete ammonia-oxidizing (comammox) bacteria widespread in terrestrial ecosystems indicates an important role of these organisms in terrestrial nitrification. Recent evidence indicated a higher ammonia affinity of comammox bacteria than of terrestrial AOA and ammonia-oxidizing bacteria (AOB), suggesting that comammox bacteria could potentially represent the most low-nutrient adapted nitrifiers in terrestrial systems. We hypothesized that a nutrient-limited enrichment strategy could exploit the differences in cellular kinetic properties and yield enrichments dominated by high affinity and high yield comammox bacteria. Using soil with a mixed community of AOA, AOB, and comammox Nitrospira, we compared performance of nutrient-limited chemostat enrichment with or without batch culture pre-enrichment in two different growth media without inhibitors or antibiotics. Monitoring of microbial community composition via 16S rRNA and amoA gene sequencing showed that batch enrichments were dominated by AOB, accompanied by low numbers of AOA and comammox Nitrospira. In contrast, nutrient-limited enrichment directly from soil, and nutrient-limited sub-cultivation of batch enrichments consistently yielded high enrichments of Nitrosocosmicus-affiliated AOA associated with multiple canonical nitrite-oxidizing Nitrospira strains, whereas AOB numbers dropped below 0.1% and comammox Nitrospira were lost completely. Our results reveal competitiveness of Nitrosocosmicus sp. under nutrient limitation, and a likely more complex or demanding ecological niche of soil comammox Nitrospira than simulated in our nutrient-limited chemostat experiments.

scholarly journals Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities

2021 ◽  
Author(s):  
Man-Young Jung ◽  
Christopher J. Sedlacek ◽  
K. Dimitri Kits ◽  
Anna J. Mueller ◽  
Sung-Keun Rhee ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Oxidation Kinetic ◽  
Ammonia Oxidizer ◽  
Substrate Affinity ◽  
Kinetic Properties ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Kinetic Measurements ◽  
Ammonia Oxidizing Archaea ◽  
Wide Range

AbstractNitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co- occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest substrate affinity of any characterized AOA, which are similar to previously determined affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values strongly supports the hypothesis that – like for AOB – ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

scholarly journals Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil

2011 ◽  
Vol 77 (18) ◽  
pp. 6551-6558 ◽  
Author(s):  
John J. Kelly ◽  
Katherine Policht ◽  
Tanya Grancharova ◽  
Lakhwinder S. Hundal
Keyword(s):  
Agricultural Soil ◽  
Terrestrial Ecosystems ◽  
Gene Copy ◽  
Ecological Niches ◽  
Corn Yield ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizing Archaea ◽  
Copy Numbers ◽  
Synthetic Fertilizer ◽  
Gene Copy Numbers

ABSTRACTThe recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically digested biosolids or synthetic fertilizer was applied annually for three consecutive years to field plots used for corn production. Biosolids were applied at two loading rates, a typical agronomic rate (27 Mg hectare−1year−1) and double the agronomic rate (54 Mg hectare−1year−1), while synthetic fertilizer was applied at an agronomic rate typical for the region (291 kg N hectare−1year−1). Both biosolids amendments and synthetic fertilizer increased soil N and corn yield, but only the biosolids amendments resulted in significant increases in nitrification rates and increases in the copy numbers of archaeal and bacterialamoAgenes. In addition, only archaealamoAgene copy numbers increased in response to biosolids applied at the typical agronomic rate and showed a significant correlation with nitrification rates. Finally, copy numbers of archaealamoAgenes were significantly higher than copy numbers of bacterialamoAgenes for all treatments. These results implicate AOA as being primarily responsible for the increased nitrification observed in an agricultural soil amended with biosolids. These results also support the hypothesis that physiological differences between AOA and AOB may enable them to occupy distinct ecological niches.

scholarly journals Autotrophic Growth of Bacterial and Archaeal Ammonia Oxidizers in Freshwater Sediment Microcosms Incubated at Different Temperatures

2013 ◽  
Vol 79 (9) ◽  
pp. 3076-3084 ◽  
Author(s):  
Yucheng Wu ◽  
Xiubin Ke ◽  
Marcela Hernández ◽  
Baozhan Wang ◽  
Marc G. Dumont ◽  
...  
Keyword(s):  
Lake Taihu ◽  
Microbial Community Composition ◽  
Stable Isotope Probing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Autotrophic Growth ◽  
Ammonia Oxidizing Archaea ◽  
Different Temperatures

ABSTRACTBoth bacteria and archaea potentially contribute to ammonia oxidation, but their roles in freshwater sediments are still poorly understood. Seasonal differences in the relative activities of these groups might exist, since cultivated archaeal ammonia oxidizers have higher temperature optima than their bacterial counterparts. In this study, sediment collected from eutrophic freshwater Lake Taihu (China) was incubated at different temperatures (4°C, 15°C, 25°C, and 37°C) for up to 8 weeks. We examined the active bacterial and archaeal ammonia oxidizers in these sediment microcosms by using combined stable isotope probing (SIP) and molecular community analysis. The results showed that accumulation of nitrate in microcosms correlated negatively with temperature, although ammonium depletion was the same, which might have been related to enhanced activity of other nitrogen transformation processes. Incubation at different temperatures significantly changed the microbial community composition, as revealed by 454 pyrosequencing targeting bacterial 16S rRNA genes. After 8 weeks of incubation, [13C]bicarbonate labeling of bacterialamoAgenes, which encode the ammonia monooxygenase subunit A, and an observed increase in copy numbers indicated the activity of ammonia-oxidizing bacteria in all microcosms.Nitrosomonassp. strain Is79A3 andNitrosomonas communislineages dominated the heavy fraction of CsCl gradients at low and high temperatures, respectively, indicating a niche differentiation of active bacterial ammonia oxidizers along the temperature gradient. The13C labeling of ammonia-oxidizing archaea in microcosms incubated at 4 to 25°C was minor. In contrast, significant13C labeling ofNitrososphaera-like archaea and changes in the abundance and composition of archaealamoAgenes were observed at 37°C, implicating autotrophic growth of ammonia-oxidizing archaea under warmer conditions.

scholarly journals Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Laibin Huang ◽  
Seemanti Chakrabarti ◽  
Jennifer Cooper ◽  
Ana Perez ◽  
Sophia M. John ◽  
...  
Keyword(s):  
Nitrogen Cycle ◽  
Agricultural Soil ◽  
Agricultural Soils ◽  
Ammonia Oxidizing Bacteria ◽  
Central Process ◽  
Soil Nitrification ◽  
Plant Nitrogen ◽  
Ammonia Oxidizing Archaea ◽  
Activity Measurements ◽  
Nitrite Oxidizing Bacteria

AbstractNitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O–N per µg NOx–N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.

scholarly journals The Role of the Reactive Species Involved in the Photocatalytic Degradation of HDPE Microplastics Using C,N-TiO2 Powders

Polymers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 999 ◽  
Author(s):  
Aranza Denisse Vital-Grappin ◽  
Maria Camila Ariza-Tarazona ◽  
Valeria Montserrat Luna-Hernández ◽  
Juan Francisco Villarreal-Chiu ◽  
Juan Manuel Hernández-López ◽  
...  
Keyword(s):  
Wastewater Treatment Plants ◽  
Reaction System ◽  
Terrestrial Ecosystems ◽  
Degradation Process ◽  
Reactive Species ◽  
Hazardous Substances ◽  
Wide Range ◽  
Degradation Behaviors ◽  
Environmentally Friendly Process

Microplastics (MPs) are distributed in a wide range of aquatic and terrestrial ecosystems throughout the planet. They are known to adsorb hazardous substances and can transfer them across the trophic web. To eliminate MPs pollution in an environmentally friendly process, we propose using a photocatalytic process that can easily be implemented in wastewater treatment plants (WWTPs). As photocatalysis involves the formation of reactive species such as holes (h+), electrons (e−), hydroxyl (OH●), and superoxide ion (O2●−) radicals, it is imperative to determine the role of those species in the degradation process to design an effective photocatalytic system. However, for MPs, this information is limited in the literature. Therefore, we present such reactive species’ role in the degradation of high-density polyethylene (HDPE) MPs using C,N-TiO2. Tert-butanol, isopropyl alcohol (IPA), Tiron, and Cu(NO3)2 were confirmed as adequate OH●, h+, O2●− and e− scavengers. These results revealed for the first time that the formation of free OH● through the pathways involving the photogenerated e− plays an essential role in the MPs’ degradation. Furthermore, the degradation behaviors observed when h+ and O2●− were removed from the reaction system suggest that these species can also perform the initiating step of degradation.

scholarly journals Gut microbiota accelerates cisplatin-induced acute liver injury associated with robust inflammation and oxidative stress in mice

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Shenhai Gong ◽  
Yinglin Feng ◽  
Yunong Zeng ◽  
Huanrui Zhang ◽  
Meiping Pan ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Metabolomic Analysis ◽  
Rrna Gene Sequencing ◽  
And Oxidative Stress

Abstract Background Gut microbiota has been reported to be disrupted by cisplatin, as well as to modulate chemotherapy toxicity. However, the precise role of intestinal microbiota in the pathogenesis of cisplatin hepatotoxicity remains unknown. Methods We compared the composition and function of gut microbiota between mice treated with and without cisplatin using 16S rRNA gene sequencing and via metabolomic analysis. For understanding the causative relationship between gut dysbiosis and cisplatin hepatotoxicity, antibiotics were administered to deplete gut microbiota and faecal microbiota transplantation (FMT) was performed before cisplatin treatment. Results 16S rRNA gene sequencing and metabolomic analysis showed that cisplatin administration caused gut microbiota dysbiosis in mice. Gut microbiota ablation by antibiotic exposure protected against the hepatotoxicity induced by cisplatin. Interestingly, mice treated with antibiotics dampened the mitogen-activated protein kinase pathway activation and promoted nuclear factor erythroid 2-related factor 2 nuclear translocation, resulting in decreased levels of both inflammation and oxidative stress in the liver. FMT also confirmed the role of microbiota in individual susceptibility to cisplatin-induced hepatotoxicity. Conclusions This study elucidated the mechanism by which gut microbiota mediates cisplatin hepatotoxicity through enhanced inflammatory response and oxidative stress. This knowledge may help develop novel therapeutic approaches that involve targeting the composition and metabolites of microbiota.

scholarly journals High yield synthesis of high-silica chabazite by combining the role of zeolite precursors and tetraethylammonium: SCR of NOx

2015 ◽  
Vol 51 (49) ◽  
pp. 9965-9968 ◽  
Author(s):  
Nuria Martín ◽  
Manuel Moliner ◽  
Avelino Corma
Keyword(s):  
High Yield ◽  
High Solid ◽  
Rational Combination ◽  
High Silica ◽  
Scr Of Nox ◽  
Zeolite Precursors

The synthesis of chabazite with high solid yields is achieved by the rational combination of directing effects of a source of Si and Al coming from USY zeolites and the inexpensive tetraethylammonium.

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