scholarly journals Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils

2016 ◽  
Vol 82 (10) ◽  
pp. 2919-2928 ◽  
Author(s):  
Steven A. Higgins ◽  
Allana Welsh ◽  
Luis H. Orellana ◽  
Konstantinos T. Konstantinidis ◽  
Joanne C. Chee-Sanford ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Agricultural Soils ◽  
Agricultural Practices ◽  
Environmental Dna ◽  
Pcr Primers ◽  
Amino Acid Identity ◽  
N Loss ◽  
Content Type ◽  
Denitrification Potential ◽  
Fungal Isolates

ABSTRACTMembers of the Fungi convert nitrate (NO3−) and nitrite (NO2−) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations, and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N2O from added NO3−or NO2−in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, 151 of which produced N2O from NO2−. Novel PCR primers targeting thep450norgene, which encodes the nitric oxide (NO) reductase responsible for N2O production in fungi, yielded 26 novelp450noramplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54 to 98% amino acid identity with reference P450nor sequences within the phylumAscomycotaand expand the known fungal P450nor sequence diversity.p450norwas detected in all fungal isolates that produced N2O from NO2−, whereasnirK(encoding the NO-forming NO2−reductase) was amplified in only 13 to 74% of the N2O-forming isolates using two separatenirKprimer sets. Collectively, our findings demonstrate the value ofp450nor-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N2O formation.IMPORTANCEA comprehensive understanding of the microbiota controlling soil N loss and greenhouse gas (N2O) emissions is crucial for sustainable agricultural practices and addressing climate change concerns. We report the design and application of a novel PCR primer set targeting fungalp450nor, a biomarker for fungal N2O production, and demonstrate the utility of the new approach to assess fungal denitrification potential in fungal isolates and agricultural soils. These new PCR primers may find application in a variety of biomes to assess the fungal contributions to N loss and N2O emissions.

scholarly journals NovelP450norGene Detection Assay Used To Characterize the Prevalence and Diversity of Soil Fungal Denitrifiers

2016 ◽  
Vol 82 (15) ◽  
pp. 4560-4569 ◽  
Author(s):  
Amy Novinscak ◽  
Claudia Goyer ◽  
Bernie J. Zebarth ◽  
David L. Burton ◽  
Martin H. Chantigny ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Agricultural Soils ◽  
Pcr Primers ◽  
Soil Samples ◽  
Pcr Assay ◽  
Gene Encoding ◽  
Content Type ◽  
Soil Ecosystems ◽  
Detection Assay ◽  
Denitrification Genes

ABSTRACTDenitrifying fungi produce nitrous oxide (N2O), a potent greenhouse gas, as they generally lack the ability to convert N2O to dinitrogen. Contrary to the case for bacterial denitrifiers, the prevalence and diversity of denitrifying fungi found in the environment are not well characterized. In this study, denitrifying fungi were isolated from various soil ecosystems, and novel PCR primers targeting theP450norgene, encoding the enzyme responsible for the conversion of nitric oxide to N2O, were developed, validated, and used to study the diversity of cultivable fungal denitrifiers. This PCR assay was also used to detectP450norgenes directly from environmental soil samples. Fungal denitrification capabilities were further validated using an N2O gas detection assay and a PCR assay targeting thenirKgene. A collection of 492 facultative anaerobic fungi was isolated from 15 soil ecosystems and taxonomically identified by sequencing the internal transcribed spacer sequence. Twenty-seven fungal denitrifiers belonging to 10 genera had theP450norand thenirKgenes and produced N2O from nitrite. N2O production is reported in strains not commonly known as denitrifiers, such asByssochlamys nivea,Volutella ciliata,Chloridiumspp., andTrichocladiumspp. The prevalence of fungal denitrifiers did not follow a soil ecosystem distribution; however, a higher diversity was observed in compost and agricultural soils. The phylogenetic trees constructed using partialP450norandnirKgene sequences revealed that both genes clustered taxonomically closely related strains together.IMPORTANCEA PCR assay targeting theP450norgene involved in fungal denitrification was developed and validated. The newly developedP450norprimers were used on fungal DNA extracted from a collection of fungi isolated from various soil environments and on DNA directly extracted from soil. The results indicated that approximatively 25% of all isolated fungi possessed this gene and were able to convert nitrite to N2O. All soil samples from which denitrifying fungi were isolated also tested positive for the presence ofP450nor. TheP450norgene detection assay was reliable in detecting a large diversity of fungal denitrifiers. Due to the lack of homology existing betweenP450norand bacterial denitrification genes, it is expected that this assay will become a tool of choice for studying fungal denitrifiers.

scholarly journals Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Christopher J. Sedlacek ◽  
Andrew T. Giguere ◽  
Michael D. Dobie ◽  
Brett L. Mellbye ◽  
Rebecca V. Ferrell ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Nitrous Oxide ◽  
Agricultural Soils ◽  
Nitrosomonas Europaea ◽  
Oxygen Limitation ◽  
Ammonia Oxidizing Bacteria ◽  
Content Type ◽  
Nitrifier Denitrification ◽  
Nitrous Oxide Production ◽  
Effect Of Oxygen

ABSTRACT Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea’s sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria. IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

scholarly journals Denitrification byAnaeromyxobacter dehalogenans, a Common Soil Bacterium Lacking the Nitrite Reductase GenesnirSandnirK

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Jenny R. Onley ◽  
Samiha Ahsan ◽  
Robert A. Sanford ◽  
Frank E. Löffler
Keyword(s):  
Soil Bacterium ◽  
Reference Sequence ◽  
Bacterial Genomes ◽  
N Loss ◽  
Content Type ◽  
Denitrification Potential ◽  
Soil Ecosystems ◽  
New Findings ◽  
Soils And Sediments ◽  
Denitrification Genes

ABSTRACTThe versatile soil bacteriumAnaeromyxobacter dehalogenanslacks the hallmark denitrification genesnirSandnirK(encoding NO2−→NO reductases) and couples growth to NO3−reduction to NH4+(respiratory ammonification) and to N2O reduction to N2.A. dehalogenansalso grows by reducing Fe(III) to Fe(II), which chemically reacts with NO2−to form N2O (i.e., chemodenitrification). Following the addition of 100 μmol of NO3−or NO2−to Fe(III)-grown axenic cultures ofA. dehalogenans, 54 (±7) μmol and 113 (±2) μmol N2O-N, respectively, were produced and subsequently consumed. The conversion of NO3−to N2in the presence of Fe(II) through linked biotic-abiotic reactions represents an unrecognized ecophysiology ofA. dehalogenans. The new findings demonstrate that the assessment of gene content alone is insufficient to predict microbial denitrification potential and N loss (i.e., the formation of gaseous N products). A survey of complete bacterial genomes in the NCBI Reference Sequence database coupled with available physiological information revealed that organisms lackingnirSornirKbut with Fe(III) reduction potential and genes for NO3−and N2O reduction are not rare, indicating that NO3−reduction to N2through linked biotic-abiotic reactions is not limited toA. dehalogenans. Considering the ubiquity of iron in soils and sediments and the broad distribution of dissimilatory Fe(III) and NO3−reducers, denitrification independent of NO-forming NO2−reductases (through combined biotic-abiotic reactions) may have substantial contributions to N loss and N2O flux.IMPORTANCECurrent attempts to gauge N loss from soils rely on the quantitative measurement ofnirKandnirSgenes and/or transcripts. In the presence of iron, the common soil bacteriumAnaeromyxobacter dehalogenansis capable of denitrification and the production of N2without the key denitrification genesnirKandnirS. Such chemodenitrifiers denitrify through combined biotic and abiotic reactions and have potentially large contributions to N loss to the atmosphere and fill a heretofore unrecognized ecological niche in soil ecosystems. The findings emphasize that the comprehensive understanding of N flux and the accurate assessment of denitrification potential can be achieved only when integrated studies of interlinked biogeochemical cycles are performed.

Agricultural practices and diffuse nitrogen pollution in Denmark: empirical leaching and catchment models

1999 ◽  
Vol 39 (12) ◽  
pp. 257-264 ◽  
Author(s):  
Hans E. Andersen ◽  
Brian Kronvang ◽  
Søren E. Larsen
Keyword(s):  
Agricultural Land ◽  
Root Zone ◽  
Agricultural Practices ◽  
Animal Manure ◽  
Annual Runoff ◽  
N Leaching ◽  
N Loss ◽  
Total N ◽  
Model Calculations ◽  
N Removal

An empirical leaching model was applied to data on agricultural practices at the field level within 6 small Danish agricultural catchments in order to document any changes in nitrogen (N) leaching from the root zone during the period 1989-96. The model calculations performed at normal climate revealed an average reduction in N-leaching that amounted to 30% in the loamy catchments and 9% in the sandy catchments. The reductions in N leaching could be ascribed to several improvements in agricultural practices during the study period: (i) regulations on livestock density; (ii) regulations on the utilisation of animal manure; (iii) regulations concerning application practices for manure. The average annual total N-loss from agricultural areas to surface water constituted only 54% of the annual average N leached from the root zone in the three loamy catchments and 17% in the three sandy catchments. Thus, subsurface N-removal processes are capable of removing large amounts of N leached from agricultural land. An empirical model for the annual diffuse N-loss to streams from small catchments is presented. The model predicts annual N-loss as a function of the average annual use of mineral fertiliser and manure in the catchment and the total annual runoff from the unsaturated zone.

scholarly journals Long-Read Amplicon Sequencing of Nitric Oxide Dismutase (nod) Genes Reveal Diverse Oxygenic Denitrifiers in Agricultural Soils and Lake Sediments

2020 ◽  
Vol 80 (1) ◽  
pp. 243-247 ◽  
Author(s):  
Baoli Zhu ◽  
Zhe Wang ◽  
Dheeraj Kanaparthi ◽  
Susanne Kublik ◽  
Tida Ge ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Lake Sediments ◽  
Agricultural Soils ◽  
Amplicon Sequencing ◽  
Nod Genes ◽  
Long Read

scholarly journals Musculoskeletal disorders among rice farmers in Phimai District, Nakhon Ratchasima Province, Thailand

2019 ◽  
Vol 33 (6) ◽  
pp. 494-503
Author(s):  
Ekarat Sombatsawat ◽  
Titaporn Luangwilai ◽  
Parichat Ong-artborirak ◽  
Wattasit Siriwong
Keyword(s):  
Musculoskeletal Disorders ◽  
Work Experience ◽  
Rank Correlation ◽  
Agricultural Practices ◽  
Farm Size ◽  
Body Region ◽  
Cross Sectional ◽  
Content Type ◽  
Rice Farmers ◽  
Body Regions

Purpose The purpose of this paper is to explore the prevalence of musculoskeletal disorders (MSDs) and determine factors influencing MSDs among rice farmers. Design/methodology/approach A cross-sectional study was carried out among 156 rice farmers from 14 villages in Tarnlalord sub-district, Phimai district, Nakhon Ratchasima province, Thailand, from February 2017 to March 2017. Face-to-face interviews, including demographics, work characteristics and musculoskeletal pain, were conducted using a modified standardized Nordic questionnaire. Findings The results revealed that both 78 males and 78 females participated in the study to which the average of age and body mass index (BMI) was 45.5±11.4 years and 24.9±4.0 kg/m2, respectively. All rice farmers reported MSDs in at least one body region during the six months preceding the interview. The highest prevalence of MSDs showed 86.5 percent in the lower back area, followed by 85.9 percent in the neck, and 80.7 percent in the shoulders. The analysis of binary logistic regression and Spearman’s rank correlation showed that factors such as gender, age, BMI, work experience and farm size influence MSDs’ occurrence, and pain severity in one or more body regions (p < 0.05). Originality/value Musculoskeletal injuries are a significant health problem in rice farmers. The study indicated that appropriate agricultural practices such as working posture, equipment size selection and carrying loads should be recommended to prevent MSDs. Thus, the occupational health and safety services in agricultural workers are needed.

Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013

2021 ◽  
Vol 71 (5) ◽  
Author(s):  
Dominic A. Stoll ◽  
Nicolas Danylec ◽  
Christina Grimmler ◽  
Sabine E. Kulling ◽  
Melanie Huch
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Genome Wide ◽  
Average Amino Acid Identity ◽  
Biochemical Analyses

The strain Adlercreutzia caecicola DSM 22242T (=CCUG 57646T=NR06T) was taxonomically described in 2013 and named as Parvibacter caecicola Clavel et al. 2013. In 2018, the name of the strain DSM 22242T was changed to Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 due to taxonomic investigations of the closely related genera Adlercreutzia, Asaccharobacter and Enterorhabdus within the phylum Actinobacteria . However, the first whole draft genome of strain DSM 22242T was published by our group in 2019. Therefore, the genome was not available within the study of Nouioui et al. (2018). The results of the polyphasic approach within this study, including phenotypic and biochemical analyses and genome-based taxonomic investigations [genome-wide average nucleotide identity (gANI), alignment fraction (AF), average amino acid identity (AAI), percentage of orthologous conserved proteins (POCP) and genome blast distance phylogeny (GBDP) tree], indicated that the proposed change of the name Parvibacter caecicola to Adlercreutzia caecicola was not correct. Therefore, it is proposed that the correct name of Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 strain DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

Products, genetic linkage and limb patterning activity of a murine hedgehog gene

Development ◽  
1994 ◽  
Vol 120 (11) ◽  
pp. 3339-3353 ◽  
Author(s):  
D.T. Chang ◽  
A. Lopez ◽  
D.P. von Kessler ◽  
C. Chiang ◽  
B.K. Simandl ◽  
...  
Keyword(s):  
Limb Development ◽  
Genetic Linkage ◽  
Pcr Primers ◽  
Amino Acid Identity ◽  
Protein Product ◽  
Proteolytic Processing ◽  
Limb Bud ◽  
Gene Encoding ◽  
Mouse Limb ◽  
Drosophila Embryos

The hedgehog (hh) segmentation gene of Drosophila melanogaster encodes a secreted signaling protein that functions in the patterning of larval and adult structures. Using low stringency hybridization and degenerate PCR primers, we have isolated complete or partial hh-like sequences from a range of invertebrate species including other insects, leech and sea urchin. We have also isolated three mouse and two human DNA fragments encoding distinct hh-like sequences. Our studies have focused upon Hhg-1, a mouse gene encoding a protein with 46% amino acid identity to hh. The Hhg-1 gene, which corresponds to the previously described vhh-1 or sonic class, is expressed in the notochord, ventral neural tube, lung bud, hindgut and posterior margin of the limb bud in developing mouse embryos. By segregation analysis the Hhg-1 gene has been localized to a region in proximal chromosome 5, where two mutations affecting mouse limb development previously have been mapped. In Drosophila embryos, ubiquitous expression of the Hhg-1 gene yields effects upon gene expression and cuticle pattern similar to those observed for the Drosophila hh gene. We also find that cultured quail cells transfected with a Hhg-1 expression construct can induce digit duplications when grafted to anterior or mid-distal but not posterior borders within the developing chick limb; more proximal limb element duplications are induced exclusively by mid-distal grafts. Both in transgenic Drosophila embryos and in transfected quail cells, the Hhg-1 protein product is cleaved to yield two stable fragments from a single larger precursor. The significance of Hhg-1 genetic linkage, patterning activity and proteolytic processing in Drosophila and chick embryos is discussed.

Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacterium and Ruania are heterotypic synonyms and description of Occultella aeris sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Peter Schumann ◽  
Franziska Kalensee ◽  
Jialan Cao ◽  
Alexis Criscuolo ◽  
Dominique Clermont ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Copper Smelter ◽  
Amino Acid Identity ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Emended Description ◽  
Copper Mines

In the course of screening the surface soils of ancient copper mines and smelters (East Harz, Germany) an aerobic, non-motile and halotolerant actinobacterium forming small rods or cocci was isolated. The strain designated F300T developed creamy to yellow colonies on tryptone soy agar and grew optimally at 28 °C, pH 7–8 and with 0.5–2 % (m/v) NaCl. Its peptidoglycan was of type A4α l-Lys–l-Glu (A11.54). The menaquinone profile was dominated by MK-8(II, III-H4) and contained minor amounts of MK-8(H2), MK-8(H6) and MK-9(H4). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, mono and diacylated phosphatidylinositol dimannosides, and components that were not fully characterized, including two phospholipids, two glycolipids and an uncharacterized lipid. Major whole-cell sugars were rhamnose and ribose. The fatty acid profile contained mainly iso and anteiso branched fatty acids (anteiso-C15 : 0, iso-C14 : 0) and aldehydes/dimethylacetals (i.e. not fatty acids). Sequence analysis of its genomic DNA and subsequent analysis of the data placed the isolate in the group currently defined by members of the genera Ruania and Haloactinobacterium (family Ruaniaceae , order Micrococcales ) as a sister taxon to the previously described species Haloactinobacterium glacieicola , sharing an average nucleotide identity and average amino acid identity values of 85.3 and 85.7 %, respectively. Genotypic and chemotaxonomic analyses support the view that strain F300T (=DSM 108350T=CIP 111667T) is the type strain of a new genus and new species for which the name Occultella aeris gen. nov., sp. nov. is proposed. Based on revised chemotaxonomic and additional genome based data, it is necessary to discuss and evaluate the results in the light of the classification and nomenclature of members of the family Ruaniaceae , i.e. the genera Haloactinobacterium and Ruania . Consequently, the reclassification of Haloactinobacterium glacieicola as Occultella glacieicola comb. nov. and Haloactinobacterium album as Ruania alba comb. nov., with an emended description of the genus Ruania are proposed.

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