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 Nitrogen fixation and the diazotroph community in the temperate coastal region of the northwestern North Pacific

2015 ◽  
Vol 12 (15) ◽  
pp. 4751-4764 ◽  
Author(s):  
T. Shiozaki ◽  
T. Nagata ◽  
M. Ijichi ◽  
K. Furuya
Keyword(s):  
Nitrogen Fixation ◽  
North Pacific ◽  
Nifh Gene ◽  
Anaerobic Bacteria ◽  
Coastal Region ◽  
Late Summer ◽  
Euphotic Zone ◽  
Early Summer ◽  
Pcr Analysis ◽  
Subsurface Layers

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 the diazotroph community within the euphotic zone in the temperate coastal region of the northwestern North Pacific. Nitrogen fixation as high as 13.6 nmol N L−1 d−1 was measured from early summer to fall when the surface temperature exceeded 14.2 °C (but was lower than 24.3 °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). Clone library analysis results indicated that nifH gene sequences were omnipresent throughout the investigation period. During the period when nitrogen fixation was detected (early summer to fall), the genes affiliated with UCYN-A, Trichodesmium, and γ-proteobacterial phylotype γ-24774A11 were frequently recovered. In contrast, when nitrogen fixation was undetectable (winter to spring), many sequences affiliated with Cluster III diazotrophs (putative anaerobic bacteria) were recovered. Quantitative PCR analysis revealed that UCYN-A was relatively abundant from early to late summer compared with Trichodesmium and γ-24774A11, whereas Trichodesmium abundance was the highest among the three groups during fall.

Molecular identification of diazotroph microbial consortia in mountain soil

2010 ◽  
Vol 5 (5) ◽  
pp. 664-673 ◽  
Author(s):  
Rahela Carpa ◽  
Anca Butiuc-Keul ◽  
Cristina Dobrotă ◽  
Vasile Muntean
Keyword(s):  
Gene Diversity ◽  
Nifh Gene ◽  
Flood Plain ◽  
Soil Samples ◽  
Microbial Consortia ◽  
Nitrogen Fixing ◽  
Vegetation Zone ◽  
Vegetation Zones ◽  
Primer Sets ◽  
Nifh Genes

AbstractNitrogen fixing microbial consortia from soil samples taken from five altitudinal vegetation zones (alpine, subalpine, coniferous, beech, Maleia flood plain) of Parâng Massif, Romania, were isolated and identified. Molecular characterisation of nitrogen fixing consortia was carried out by PCR and nested PCR with 7 primer sets specific to nifH genes. All nifH genes are specific to nitrogen fixation and are found within phylogenetically related organisms which have the nitrogenase enzyme complex. These molecular studies allowed the assessment of nifH gene diversity within these nitrogen fixing microbial consortia from different type of soils. At high altitude, a consortium of nitrogen fixing bacteria dominated by Azotobacter chroococcum and Azospirillum brasilense was found. Clostridium, Rhizobiales, Herbaspirillum, Frankia species were also found in different rations depending on the altitudinal vegetation zone.

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.

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.

scholarly journals Mutation in the ntrR Gene, a Member of the vap Gene Family, Increases the Symbiotic Efficiency of Sinorhizobium meliloti

2001 ◽  
Vol 14 (7) ◽  
pp. 887-894 ◽  
Author(s):  
Boglárka Oláh ◽  
Erno Kiss ◽  
Zoltán Györgypál ◽  
Judit Borzi ◽  
Gyöngyi Cinege ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Pathogenic Bacteria ◽  
Sinorhizobium Meliloti ◽  
Root Nodules ◽  
Nifh Gene ◽  
Dry Weight ◽  
Nodule Occupancy ◽  
Gene Encoding ◽  
Symbiotic Efficiency ◽  
Host Interactions

In specific plant organs, namely the root nodules of alfalfa, fixed nitrogen (ammonia) produced by the symbiotic partner Sinorhizobium meliloti supports the growth of the host plant in nitrogen-depleted environment. Here, we report that a derivative of S. meliloti carrying a mutation in the chromosomal ntrR gene induced nodules with enhanced nitrogen fixation capacity, resulting in an increased dry weight and nitrogen content of alfalfa. The efficient nitrogen fixation is a result of the higher expression level of the nifH gene, encoding one of the subunits of the nitrogenase enzyme, and nifA, the transcriptional regulator of the nif operon. The ntrR gene, controlled negatively by its own product and positively by the symbiotic regulator syrM, is expressed in the same zone of nodules as the nif genes. As a result of the nitrogen-tolerant phenotype of the strain, the beneficial effect of the mutation on efficiency is not abolished in the presence of the exogenous nitrogen source. The ntrR mutant is highly competitive in nodule occupancy compared with the wild-type strain. Sequence analysis of the mutant region revealed a new cluster of genes, termed the “ntrPR operon,” which is highly homologous to a group of vap-related genes of various pathogenic bacteria that are presumably implicated in bacterium-host interactions. On the basis of its favorable properties, the strain is a good candidate for future agricultural utilization.

scholarly journals Euphotic zone metabolism in the North Pacific Subtropical Gyre based on oxygen dynamics

2020 ◽  
Author(s):  
Sara Ferron ◽  
Benedetto Barone ◽  
Matthew J Church ◽  
Angelicque E. White ◽  
David M. Karl
Keyword(s):  
North Pacific ◽  
Euphotic Zone ◽  
Subtropical Gyre ◽  
North Pacific Subtropical Gyre ◽  
The North ◽  
Oxygen Dynamics ◽  
The North Pacific

scholarly journals Biological nitrogen fixation in the oxygen-minimum region of the eastern tropical North Pacific ocean

2017 ◽  
Vol 11 (10) ◽  
pp. 2356-2367 ◽  
Author(s):  
Amal Jayakumar ◽  
Bonnie X Chang ◽  
Brittany Widner ◽  
Peter Bernhardt ◽  
Margaret R Mulholland ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Pacific Ocean ◽  
North Pacific ◽  
Biological Nitrogen Fixation ◽  
North Pacific Ocean ◽  
Biological Nitrogen ◽  
Oxygen Minimum

scholarly journals Trichome Lengths of the Heterocystous N2-Fixing Cyanobacteria in the Tropical Marginal Seas of the Western North Pacific

2021 ◽  
Vol 8 ◽  
Author(s):  
Sing-how Tuo ◽  
Margaret R. Mulholland ◽  
Yukiko Taniuchi ◽  
Houng-Yung Chen ◽  
Wann-Neng Jane ◽  
...  
Keyword(s):  
North Pacific ◽  
Western North Pacific ◽  
Euphotic Zone ◽  
Nutrient Concentrations ◽  
Gas Vesicles ◽  
Filamentous Cyanobacteria ◽  
Cool Season ◽  
Free Living ◽  
Marginal Seas ◽  
Tropical Oceans

Calothrix rhizosoleniae and Richelia intracellularis are heterocystous cyanobacteria found in the tropical oceans. C. rhizosoleniae commonly live epiphytically on diatom genera Chaetoceros (C-C) and Bacteriastrum (B-C) while R. intracellularis live endosymbiotically within Rhizosolenia (R-R), Guinardia (G-R), and Hemiaulus (H-R); although, they occasionally live freely (FL-C and FL-R). Both species have much shorter trichomes than the other marine filamentous cyanobacteria such as Trichodesmium spp. and Anabaena gerdii. We investigated the trichome lengths of C. rhizosoleniae and R. intracellularis in the South China Sea (SCS) and the Philippine Sea (PS) between 2006 and 2014. On average, H-R had the shortest trichome lengths (3.5 cells/trichome), followed by B-C and C-C (4.9–5.2 cells/trichome) and FL-C (5.9 cells/trichome), and R-R, G-R, and FL-R had the longest trichome lengths (7.4–8.3 cells/trichome). Field results showed the trichome lengths of C-C and B-C did not vary seasonally or regionally. However, FL-C and H-R from the SCS and during the cool season had longer trichomes, where/when the ambient nutrient concentrations were higher. R-R, G-R, and FL-R also showed regional and seasonal variations in trichome length. Ultrastructural analysis found no gas vesicles within the C. rhizosoleniae cells to assist in buoyancy regulation. Results suggest that the trichome lengths of C. rhizosoleniae and R. intracellularis might be regulated by their diatom hosts’ symbiotic styles and by ambient nutrients. Short trichome length might help C. rhizosoleniae and R. intracellularis to stay in the euphotic zone regardless as to whether they are free-living or symbiotic.

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