Ammonia oxidation (amoA) and nitrogen fixation (nifH) genes along metasandstone and limestone caves of Brazil

2018 ◽  
Vol 35 (10) ◽  
pp. 869-878 ◽  
Author(s):  
Eric de Lima Silva Marques ◽  
Eduardo Gross ◽  
João Carlos Teixeira Dias ◽  
Carlos Priminho Pirovani ◽  
Rachel Passos Rezende
Keyword(s):  
Nitrogen Fixation ◽  
Ammonia Oxidation ◽  
Nifh Genes

scholarly journals Diversity of Ammonia Oxidation (amoA) and Nitrogen Fixation (nifH) Genes in Lava Caves of Terceira, Azores, Portugal

2014 ◽  
Vol 31 (3) ◽  
pp. 221-235 ◽  
Author(s):  
Jennifer J. Marshall Hathaway ◽  
Robert L. Sinsabaugh ◽  
Maria De Lurdes N. E. Dapkevicius ◽  
Diana E. Northup
Keyword(s):  
Nitrogen Fixation ◽  
Ammonia Oxidation ◽  
Nifh Genes

scholarly journals Seasonal dynamics of nitrogen fixation and the diazotroph community in the temperate coastal region of the northwestern North Pacific

2015 ◽  
Vol 12 (1) ◽  
pp. 865-889
Author(s):  
T. Shiozaki ◽  
T. Nagata ◽  
M. Ijichi ◽  
K. Furuya
Keyword(s):  
Nitrogen Fixation ◽  
North Pacific ◽  
Gene Diversity ◽  
Nifh Gene ◽  
Anaerobic Bacteria ◽  
Coastal Region ◽  
Euphotic Zone ◽  
Early Summer ◽  
Subsurface Layers ◽  
Nifh Genes

Abstract. Nitrogen fixation in temperate oceans is a potentially important, but poorly understood process that may influence the marine nitrogen budget. This study determined seasonal variations in nitrogen fixation and nifH gene diversity within the euphotic zone in the temperate coastal region of the northwestern North Pacific. Nitrogen fixation as high as 13.6 nmolN L−1 d−1 was measured from early summer to fall when the surface temperature exceeded 14.2 °C and the surface nitrate concentration was low (≤ 0.30 μM), although we also detected nitrogen fixation in subsurface layers (42–62 m) where nitrate concentrations were high (> 1 μM). During periods with high nitrogen fixation, the nifH sequences of UCYN-A were recovered, suggesting that these groups played a key role in nitrogen fixation. The nifH genes were also recovered in spring and winter when nitrogen fixation was undetectable. These genes consisted of many sequences affiliated with Cluster III diazotrophs (putative anaerobic bacteria), which hitherto have rarely been reported to be abundant in surface diazotroph communities in marine environments.

scholarly journals Diversity and distribution of Nitrogen Fixation Genes in the Oxygen Minimum Zones of the World Oceans

2020 ◽  
Author(s):  
Amal Jayakumar ◽  
Bess B. Ward
Keyword(s):  
Nitrogen Fixation ◽  
Surface Waters ◽  
World Ocean ◽  
Operational Taxonomic Unit ◽  
N Fixation ◽  
Oxygen Minimum Zones ◽  
Abundant Otus ◽  
The World ◽  
Nifh Genes ◽  
Oxygen Minimum

Abstract. Diversity and community composition of nitrogen fixing microbes in the three main oxygen minimum zones (OMZs) of the world ocean were investigated using operational taxonomic unit (OTU) analysis of nifH clone libraries. Representatives of the all four main clusters of nifH genes were detected. Cluster I sequences were most diverse in the surface waters and the most abundant OTUs were affiliated with Alpha- and Gammaproteobacteria. Cluster II, III, IV assemblages were most diverse at oxygen depleted depths and none of the sequences were closely related to sequences from cultivated organisms. The OTUs were biogeographically distinct for the most part – there was little overlap among regions, between depths or between cDNA and DNA. Only a few cyanobacterial sequences were detected. The prevalence and diversity of microbes that harbour nifH genes in the OMZ regions, where low rates of N fixation are reported, remains an enigma.

scholarly journals Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

2021 ◽  
Author(s):  
Tom O. Delmont ◽  
Juan Jose Pierella Karlusich ◽  
Iva Veseli ◽  
Jessika Fuessel ◽  
A. Murat Eren ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Nitrogen Balance ◽  
Large Scale ◽  
Current View ◽  
Low Oxygen ◽  
Nitrogen Fixers ◽  
Large Size ◽  
Genomic Characterization ◽  
Biological Nitrogen ◽  
Nifh Genes

Biological nitrogen fixation is a major factor contributing to microbial primary productivity in the open ocean. The current view depicts a few cyanobacterial diazotrophs as the most relevant marine nitrogen fixers, whereas heterotrophic diazotrophs are more diverse and considered to have lower impacts on the nitrogen balance. Here, we used 891 Tara Oceans metagenomes to create a manually curated, non-redundant genomic database corresponding to free-living, as well as filamentous, colony-forming, particle-attached and symbiotic bacterial and archaeal populations occurring in the surface of five oceans and two seas. Notably, the database provided the genomic content of eight cyanobacterial diazotrophs including Trichodesmium populations and a newly discovered population similar to Richelia, as well as 40 heterotrophic bacterial diazotrophs organized into three main functional groups that considerably expand the known diversity of abundant marine nitrogen fixers compared to previous genomic surveys. Critically, these 48 populations may account for more than 90% of cells containing known nifH genes and occurring in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. The newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ, and co-occur under nitrate-depleted conditions in large size fractions where they might form aggregates providing the low-oxygen microenvironments required for nitrogen fixation. Most significantly, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas. This large-scale environmental genomic survey emphasizes the considerable potential of heterotrophs in the marine nitrogen balance.

scholarly journals Competition for Ammonia Influences the Structure of Chemotrophic Communities in Geothermal Springs

2013 ◽  
Vol 80 (2) ◽  
pp. 653-661 ◽  
Author(s):  
Trinity L. Hamilton ◽  
Evangeline Koonce ◽  
Alta Howells ◽  
Jeff R. Havig ◽  
Talia Jewell ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Acetylene Reduction ◽  
Ammonia Oxidation ◽  
Hot Spring ◽  
Transcript Levels ◽  
Content Type ◽  
Geothermal Springs ◽  
Ammonia Oxidizing Archaea ◽  
Nitrite Production ◽  
N Pool

ABSTRACTSource waters sampled from Perpetual Spouter hot spring (pH 7.03, 86.4°C), Yellowstone National Park, WY, have low concentrations of total ammonia, nitrite, and nitrate, suggesting nitrogen (N) limitation and/or tight coupling of N cycling processes. Dominant small-subunit rRNA sequences in Perpetual Spouter source sediments are closely affiliated with the ammonia-oxidizing archaeon “CandidatusNitrosocaldus yellowstonii” and the putatively nitrogen-fixing (diazotrophic) bacteriumThermocrinis albus, respectively, suggesting that these populations may interact at the level of the bioavailable N pool, specifically, ammonia. This hypothesis was evaluated by using a combination of geochemical, physiological, and transcriptomic analyses of sediment microcosms. Amendment of microcosms with allylthiourea, an inhibitor of ammonia oxidation, decreased rates of acetylene reduction (a proxy for N2fixation) and nitrite production (a proxy for ammonia oxidation) and decreased transcript levels of structural genes involved in both nitrogen fixation (nifH) and ammonia oxidation (amoA). In contrast, amendment of microcosms with ammonia stimulated nitrite production and increasedamoAtranscript levels while it suppressed rates of acetylene reduction and decreasednifHtranscript levels. Sequencing of amplifiednifHandamoAtranscripts from native sediments, as well as microcosms, at 2 and 4 h postamendment, indicates that the dominant and responsive populations involved in ammonia oxidation and N2fixation are closely affiliated withCa. Nitrosocaldus yellowstonii andT. albus, respectively. Collectively, these results suggest that ammonia-oxidizing archaea, such asCa. Nitrosocaldus yellowstonii, have an apparent affinity for ammonia that is higher than that of the diazotrophs present in this ecosystem. Depletion of the bioavailable N pool through the activity of ammonia-oxidizing archaea likely represents a strong selective pressure for the inclusion of organisms capable of nitrogen fixation in geothermal communities. These observations help to explain the strong pattern in the codistribution of ammonia-oxidizing archaea and diazotrophs in circumneutral-to-alkaline geothermal springs.

scholarly journals A reduced fraction of plant N derived from atmospheric N (%Ndfa) and reduced rhizobial nifH gene numbers indicate a lower capacity for nitrogen fixation in nodules of white clover exposed to long-term CO<sub>2</sub> enrichment

2013 ◽  
Vol 10 (12) ◽  
pp. 8269-8281 ◽  
Author(s):  
T. Watanabe ◽  
S. Bowatte ◽  
P. C. D. Newton
Keyword(s):  
Nitrogen Fixation ◽  
Elevated Co2 ◽  
White Clover ◽  
Trifolium Repens ◽  
Nifh Gene ◽  
Shoot Biomass ◽  
N Fixation ◽  
Dna Amount ◽  
Trifolium Repens L ◽  
Nifh Genes

Abstract. Using the δ15N natural abundance method, we found that the fraction of nitrogen derived from atmospheric N (%Ndfa) in field-grown white clover (Trifolium repens L.) plants was significantly lower (72.0% vs. 89.8%, p = 0.047 in a grassland exposed to elevated CO2 for 13 yr using free air carbon dioxide enrichment (FACE). Twelve months later we conducted an experiment to investigate the reasons behind the reduced N fixation. We took cuttings from white clover plants growing in the FACE and established individual plants in a glasshouse using soil from the appropriate ambient or elevated CO2 treatments. The established plants were then transplanted back into their "rings of origin" and sampled over a 6-week period. We used molecular ecological analyses targeting nifH genes and transcripts of rhizobia in symbiosis with white clover (Trifolium repens L.) to understand the potential mechanisms. Shoot biomass was significantly lower in eCO2, but there was no difference in nodule number or mass per plant. The numbers of nifH genes and gene transcripts per nodule were significantly reduced under eCO2, but the ratio of gene to transcript number and the strains of rhizobia present were the same in both treatments. We conclude that the capacity for biological nitrogen fixation was reduced by eCO2 in white clover and was related to the reduced rhizobia numbers in nodules. We discuss the finding of reduced gene number in relation to factors controlling bacteroid DNA amount, which may imply an influence of nitrogen as well as phosphorus.

The nitrogen cycle

2018 ◽  
Author(s):  
David L. Kirchman
Keyword(s):  
Nitrous Oxide ◽  
Nitrogen Fixation ◽  
Nitrogen Cycle ◽  
Ammonia Oxidation ◽  
Heterotrophic Bacteria ◽  
Ammonium Nitrogen ◽  
Gas Production ◽  
Ammonia Oxidizing Bacteria ◽  
Nitrogen Gas ◽  
Chemolithoautotrophic Bacteria

Nitrogen is required for the biosynthesis of many cellular components and can take on many oxidation states, ranging from −3 to +5. Consequently, nitrogen compounds can act as either electron donors (chemolithotrophy) or electron acceptors (anaerobic respiration). The nitrogen cycle starts with nitrogen fixation, the reduction of nitrogen gas to ammonium. Nitrogen fixation is carried out only by prokaryotes, mainly some cyanobacteria and heterotrophic bacteria. The ammonium resulting from nitrogen fixation is quickly used by many organisms for biosynthesis, being preferred over nitrate as a nitrogen source. It is also oxidized aerobically by chemolithoautotrophic bacteria and archaea during the first step of nitrification. The second step, nitrite oxidation, is carried out by other bacteria not involved in ammonia oxidation, resulting in the formation of nitrate. Some bacteria are capable of carrying out both steps (“comammox”). This nitrate can then be reduced to nitrogen gas or nitrous oxide during denitrification. It can be reduced to ammonium, a process called “dissimilatory nitrate reduction to ammonium.” Nitrogen gas is also released by anaerobic oxidation of ammonium (“anammox”) which is carried out by bacteria in the Planctomycetes phylum. The theoretical contribution of anammox to total nitrogen gas release is 29%, but the actual contribution varies greatly. Another gas in the nitrogen cycle, nitrous oxide, is a greenhouse gas produced by ammonia-oxidizing bacteria and archaea. The available data indicate that the global nitrogen cycle is in balance, with losses from nitrogen gas production equaling gains via nitrogen fixation. But excess nitrogen from fertilizers is contributing to local imbalances and several environmental problems in drinking waters, reservoirs, lakes, and coastal oceans.

scholarly journals A reduced fraction of plant N derived from atmospheric N (%Ndfa) and reduced rhizobial nifH gene numbers indicate a lower capacity for nitrogen fixation in nodules of white clover exposed to long-term CO<sub>2</sub> enrichment

2013 ◽  
Vol 10 (6) ◽  
pp. 9867-9896 ◽  
Author(s):  
T. Watanabe ◽  
S. Bowatte ◽  
P. C. D. Newton
Keyword(s):  
Nitrogen Fixation ◽  
Elevated Co2 ◽  
White Clover ◽  
Trifolium Repens ◽  
Nifh Gene ◽  
Shoot Biomass ◽  
N Fixation ◽  
Dna Amount ◽  
Trifolium Repens L ◽  
Nifh Genes

Abstract. Using the δ15N natural abundance method, we found that the fraction of nitrogen derived from atmospheric N (%Ndfa) in field grown white clover (Trifolium repens L.) plants was significantly lower (72.0% vs. 89.5%, p = 0.047 in a grassland exposed to elevated CO2 for 13 yr using Free Air Carbon Dioxide Enrichment (FACE). Twelve months later we conducted an experiment to investigate the reasons behind the reduced N fixation. We took cuttings from white clover plants growing in the FACE and established individual plants in a glasshouse using soil from the appropriate ambient or elevated CO2 treatments. The established plants were then transplanted back into their "rings of origin" and sampled over a 6 week period. We used molecular ecological analyses targeting nifH genes and transcripts of rhizobia in symbiosis with white clover (Trifolium repens L.) to understand the potential mechanisms. Shoot biomass was significantly lower in eCO2 but there was no difference in nodule number or mass per plant. The numbers of nifH genes and gene transcripts per nodule were significantly reduced under eCO2 but the ratio of gene to transcript number and the strains of rhizobia present were the same in both treatments. We conclude that the capacity for biological nitrogen fixation was reduced by eCO2 in white clover and was related to the reduced rhizobia numbers in nodules. We discuss the finding of reduced gene number in relation to factors controlling bacteroid DNA amount which may imply an influence of nitrogen as well as phosphorus.

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