scholarly journals Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils

2011 ◽  
Vol 77 (13) ◽  
pp. 4618-4625 ◽  
Author(s):  
Huaiying Yao ◽  
Yangmei Gao ◽  
Graeme W. Nicol ◽  
Colin D. Campbell ◽  
James I. Prosser ◽  
...  
Keyword(s):  
Community Structure ◽  
Soil Ph ◽  
Ammonia Oxidation ◽  
Environmental Drivers ◽  
Ammonia Oxidizer ◽  
Long Term Effects ◽  
Acidic Soils ◽  
Nitrification Potential ◽  
Potential Nitrification ◽  
Orchard Soils

ABSTRACTAmmonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOBamoAgene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOAamoAsequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches.

scholarly journals Biochar Enhances Nitrous Oxide Reduction in Acidic but Not in Near-Neutral pH Soil

Soil Systems ◽  
2019 ◽  
Vol 3 (4) ◽  
pp. 69 ◽  
Author(s):  
Pujol Pereira ◽  
Léchot ◽  
Feola Conz ◽  
da Silva Cardoso ◽  
Six
Keyword(s):  
Nitrous Oxide ◽  
Community Structure ◽  
Soil Ph ◽  
N2o Emissions ◽  
Oxide Reduction ◽  
Acidic Soils ◽  
Nosz Gene ◽  
Neutral Ph ◽  
Nitrous Oxide Reduction ◽  
N2o Fluxes

We quantified nitrous oxide (N2O) fluxes and total denitrification (N2O + N2) in an acidic (Ferralsol) and a near-neutral pH soil (Cambisol) to determine whether biochar’s alkalinization effect could be the mechanism inducing potential reductions in N2O fluxes. In Ferralsol, decreases in N2O emissions and in the N2O to N2O + N2 ratio were observed in both biochar and lime treatments. In Cambisol, neither biochar nor lime decreased N2O emissions, despite significantly increasing soil pH. The abundance and community structure of nosZ gene-bearing microorganisms indicated that gene abundances did not explain biochar effects, but a higher diversity of nosZ gene-bearing microorganisms correlated to lower total denitrification. Overall, our results suggest that biochar’s potential to decrease N2O emissions, through soil alkalinization, may be more effective in acidic soils.

scholarly journals Biogeography of ammonia oxidizers in New England and Gulf of Mexico salt marshes and the potential importance of comammox

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
A. E. Bernhard ◽  
J. Beltz ◽  
A. E. Giblin ◽  
B. J. Roberts
Keyword(s):  
Gulf Of Mexico ◽  
New England ◽  
Salt Marshes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Biogeographic Patterns ◽  
Potential Nitrification

AbstractFew studies have focused on broad scale biogeographic patterns of ammonia oxidizers in coastal systems, yet understanding the processes that govern them is paramount to understanding the mechanisms that drive biodiversity, and ultimately impact ecosystem processes. Here we present a meta-analysis of 16 years of data of ammonia oxidizer abundance, diversity, and activity in New England (NE) salt marshes and 5 years of data from marshes in the Gulf of Mexico (GoM). Potential nitrification rates were more than 80x higher in GoM compared to NE marshes. However, nitrifier abundances varied between regions, with ammonia-oxidizing archaea (AOA) and comammox bacteria significantly greater in GoM, while ammonia-oxidizing bacteria (AOB) were more than 20x higher in NE than GoM. Total bacterial 16S rRNA genes were also significantly greater in GoM marshes. Correlation analyses of rates and abundance suggest that AOA and comammox are more important in GoM marshes, whereas AOB are more important in NE marshes. Furthermore, ratios of nitrifiers to total bacteria in NE were as much as 80x higher than in the GoM, suggesting differences in the relative importance of nitrifiers between these systems. Communities of AOA and AOB were also significantly different between the two regions, based on amoA sequences and DNA fingerprints (terminal restriction fragment length polymorphism). Differences in rates and abundances may be due to differences in salinity, temperature, and N loading between the regions, and suggest significantly different N cycling dynamics in GoM and NE marshes that are likely driven by strong environmental differences between the regions.

scholarly journals Effects of Continuous Cropping on Bacterial Community Structure in Rhizospheric Soil of Sweet Potato 

2020 ◽  
Author(s):  
Zhiyuan Gao ◽  
Yaya Hu ◽  
Meikun Han ◽  
Junjie Xu ◽  
Xue Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Sweet Potato ◽  
Soil Ph ◽  
Bacterial Community Structure ◽  
Continuous Cropping ◽  
Rhizospheric Soil ◽  
Sweet Potatoes ◽  
Potato Varieties ◽  
Soil Bacterial Community Structure

Abstract Background: Continuous cropping obstacles from sweet potato are widespread, which seriously reduce the yield and quality, cause certain economic losses. Bacteria of Rhizospheric soil are the richest and are associated with obstacles to continuous cropping. However, few studies on how continuous sweet potato cropping affects the rhizospheric soil bacterial community structure. In the study, Illumina Miseq method was used to explore rhizosphere soil bacterial community structure changes with different sweet potato varieties, and the correlation between soil characteristics and this bacterial community after continuous cropping, to provide theoretical guidance for prevention and treatment of sweet potatoes continuous cropping obstacles. Results: After continuous cropping two years, the results showed that (1) the dominant bacterial phlya in rhizospheric soils from both Xushu18 and Yizi138 were Proteobacteria, Acidobacteria, and Actinobacteria. The most dominant genus was Subgroup 6_norank. The relative abundance of rhizospheric soil bacteria of two sweet potato varieties changed significantly. (2) The richness and diversity indexes of bacteria in Xushu18 rhizospheric soil were higher than those from Yizi138 after continuous cropping. Moreover, the beneficial Lysobacter and Bacillus were more prevalent in Xushu18, but Yizi138 contained more harmful Gemmatimonadetes. (3) Soil pH decreased after continuous cropping, and redundancy analysis result indicated that soil pH was correlated significantly with bacterial community. Spearman’s rank correlations coefficients analysis demonstrated that pH was positively associated with Planctomycetes and Acidobacteria, but negatively associated with Actinobacteria and Firmicutes.Conclusions: After continuous cropping, the bacterial community structure and physicochemical properties of sweet potato rhizospheric soil were unbalanced, and the changes from different sweet potato varieties were different. The contents of Lysobacter and Bacillus were higher in the sweet potato variety resistant to continuous cropping. It provides a basis for developing new microbial fertilizer for sweet potatoes to alleviate continuous cropping obstacle.

scholarly journals Effects of Continuous Cropping on Bacterial Community Structure in Rhizospheric Soil of Sweet Potato

2020 ◽  
Author(s):  
Zhiyuan Gao ◽  
Yaya Hu ◽  
Meikun Han ◽  
Junjie Xu ◽  
Xue Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Sweet Potato ◽  
Soil Ph ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Potato Industry ◽  
Continuous Cropping ◽  
Rhizospheric Soil ◽  
Potato Varieties

Abstract Background: Continuous cropping obstacles from sweet potato are widespread, which seriously reduce the yield and quality, restrict the sustainable development of sweet potato industry. Bacteria are the most abundant in rhizospheric soil and have a certain relationship with continuous cropping obstacles. However, there are few reports on how continuous cropping affected the bacterial community structure in the rhizospheric soil of sweet potato. In this study, high-throughput sequencing technique was used to explore the changes of rhizospheric soil bacterial community structure of different sweet potato varieties, and the correlation between soil characteristics and this bacterial community after continuous cropping, so as to provide a theoretical basis for the prevention and control of sweet potato continuous cropping obstacles.Results: After two years of continuous cropping, the results showed that (1) the dominant bacteria phlya in rhizospheric soils from both Xushu18 and Yizi138 were Proteobacteria, Acidobacteria, and Actinobacteria. The most dominant genus was Subgroup 6_norank. Significant changes in the relative abundance of rhizospheric soil bacteria were observed for two sweet potato varieties. (2) Bacterial richness and diversity indexes of rhizospheric soil from Xushu18 were higher than those from Yizi138 after continuous cropping. Moreover, the beneficial Lysobacter and Bacillus were more prevalent in Xushu18, but Yizi138 contained more harmful Gemmatimonadetes. (3) Soil pH decreased after continuous cropping, and redundancy analysis showed that soil pH was significantly correlated with bacterial community. Spearman’s rank correlations coefficients analysis demonstrated that pH was positively correlated with Planctomycetes and Acidobacteria, and negatively correlated with Actinobacteria and Firmicutes.Conclusions: After continuous cropping of sweet potato, the bacterial community structure and physicochemical properties in the rhizospheric soil were unbalanced, and the changes of different sweet potato varieties were different. The contents of Lysobacter and Bacillus were higher in the sweet potato variety resistant to continuous cropping. It provides a basis for the development of special microbial fertilizer for sweet potatoes to alleviate continuous cropping obstacle.

scholarly journals Environmental drivers of benthic community structure in a deep sub-arctic fjord system

2019 ◽  
Vol 225 ◽  
pp. 106239 ◽  
Author(s):  
Èric Jordà Molina ◽  
Marc J. Silberberger ◽  
Valentin Kokarev ◽  
Henning Reiss
Keyword(s):  
Community Structure ◽  
Benthic Community ◽  
Environmental Drivers ◽  
Benthic Community Structure ◽  
Fjord System ◽  
Arctic Fjord

scholarly journals Plant Species-Dependent Effects of Liming and Plant Residue Incorporation on Soil Bacterial Community and Activity in an Acidic Orchard Soil

2020 ◽  
Vol 10 (16) ◽  
pp. 5681
Author(s):  
Xiaodi Liu ◽  
Zengwei Feng ◽  
Yang Zhou ◽  
Honghui Zhu ◽  
Qing Yao
Keyword(s):  
Microbial Community ◽  
Organic Carbon ◽  
Community Composition ◽  
Plant Species ◽  
Soil Ph ◽  
Microbial Community Composition ◽  
Plant Residue ◽  
Acidic Soils ◽  
Residue Incorporation ◽  
Test Plants

Both liming and plant residue incorporation are widely used practices for the amelioration of acidic soils—however, the difference in their effects is still not fully understood, especially regarding the microbial community. In this study, we took the acidic soils from a subtropical orchard as target soils, and implemented liming and plant residue incorporation with a leguminous and a gramineous cover crop as test plants. After six months of growth, soil pH, total organic carbon (TOC), dissolved organic carbon (DOC) and nutrient contents were determined, soil enzymes involving C, N, P cycling were assayed, and microbial communities were also analyzed using Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). Results showed that liming was more effective in elevating soil pH, while plant residue incorporation exerted a more comprehensive influence—not only on soil pH, but also on soil enzyme activity and microbial community. PCR-DGGE analysis revealed that liming changed the microbial community structure more greatly than plant residue incorporation, while plant residue incorporation altered the microbial community composition much more than liming. The growth responses of test plants to liming and plant residue incorporation depended on plant species, indicating the necessity to select appropriate practice for a particular crop. A further, detailed investigation into the microbial community composition, and the respective functions using metagenomic approach, is also suggested.

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