scholarly journals Soil Amendments Alter Ammonia-Oxidizing Archaea and Bacteria Communities in Rain-Fed Maize Field in Semi-Arid Loess Plateau

Land ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1039
Author(s):  
Setor Kwami Fudjoe ◽  
Lingling Li ◽  
Yuji Jiang ◽  
Benjamin Karikari ◽  
Junhong Xie ◽  
...  
Keyword(s):  
Loess Plateau ◽  
Soil Amendments ◽  
Gene Copy ◽  
Cow Manure ◽  
Urea Fertilizer ◽  
Nitrification Activity ◽  
Ammonia Oxidizing Archaea ◽  
Potential Nitrification ◽  
Group I ◽  
Semi Arid

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are key drivers of nitrification in rainfed soil ecosystems. However, within a semi-arid region, the influence of different soil amendments on the composition of soil AOA and AOB communities and soil properties of rainfed maize is still unclear. Therefore, in this study, the abundance, diversity, and composition of AOA and AOB communities and the potential nitrification activity (PNA) was investigated across five soil treatments: no fertilization (NA), urea fertilizer (CF), cow manure (SM), corn stalk (MS), and cow manure + urea fertilizer (SC). The AOB amoA gene copy number was influenced significantly by fertilization treatments. The AOB community was dominated by Nitrosospira cluster 3b under the CF and SC treatments, and the AOA community was dominated by Nitrososphaera Group I.1b under the CF and NA amendments; however, manure treatments (SM, MS, and SC) did not exhibit such influence. Network analysis revealed the positive impact of some hub taxonomy on the abundance of ammonia oxidizers. Soil pH, NO3−-N, Module 3, biomass, and AOB abundance were the major variables that influenced the potential nitrification activity (PNA) within structural equation modeling. PNA increased by 142.98–226.5% under the treatments CF, SC, SM, and MS compared to NA. In contrast to AOA, AOB contributed dominantly to PNA. Our study highlights the crucial role of bacterial communities in promoting sustainable agricultural production in calcareous soils in semi-arid loess plateau environments.

scholarly journals Cultivation of Autotrophic Ammonia-Oxidizing Archaea from Marine Sediments in Coculture with Sulfur-Oxidizing Bacteria

2010 ◽  
Vol 76 (22) ◽  
pp. 7575-7587 ◽  
Author(s):  
Byoung-Joon Park ◽  
Soo-Je Park ◽  
Dae-No Yoon ◽  
Stefan Schouten ◽  
Jaap S. Sinninghe Damsté ◽  
...  
Keyword(s):  
16S Rrna ◽  
Marine Sediments ◽  
Ammonia Oxidation ◽  
Enrichment Culture ◽  
Gene Copy ◽  
Initial Growth ◽  
Ammonia Oxidizing Archaea ◽  
Group I ◽  
Sulfur Oxidizing ◽  
Sulfur Oxidizing Bacteria

ABSTRACT The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and “Candidatus Nitrosopumilus maritimus” (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichment of AOA over ammonia-oxidizing bacteria (AOB) is likely due to the reduced oxygen levels caused by the rapid initial growth of SOB. After biweekly transfers for ca. 20 months, archaeal cells became the dominant prokaryotes (>80%), based on quantitative PCR and fluorescence in situ hybridization analysis. The increase of archaeal 16S rRNA gene copy numbers was coincident with the amount of ammonia oxidized, and expression of the archaeal amoA gene was observed during ammonia oxidation. Bacterial amoA genes were not detected in the enrichment culture. The affinities of these AOA to oxygen and ammonia were substantially higher than those of AOB. [13C]bicarbonate incorporation and the presence and activation of genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle indicated autotrophy during ammonia oxidation. In the enrichment culture, ammonium was oxidized to nitrite by the AOA and subsequently to nitrate by Nitrospina-like bacteria. Our experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments.

scholarly journals Ammonium Availability Affects the Ratio of Ammonia-Oxidizing Bacteria to Ammonia-Oxidizing Archaea in Simulated Creek Ecosystems

2011 ◽  
Vol 77 (5) ◽  
pp. 1896-1899 ◽  
Author(s):  
Martina Herrmann ◽  
Andrea Scheibe ◽  
Sharon Avrahami ◽  
Kirsten Küsel
Keyword(s):  
Microbial Community ◽  
Incubation Period ◽  
Gene Copy ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizing Archaea ◽  
Flow Channels ◽  
Copy Numbers ◽  
Potential Nitrification ◽  
Gene Copy Numbers ◽  
Clay Tiles

ABSTRACTThe ammonia-oxidizing microbial community colonizing clay tiles in flow channels changed in favor of ammonia-oxidizing bacteria during a 12-week incubation period even at originally high ratios of ammonia-oxidizing archaea to ammonia-oxidizing bacteria (AOB). AOB predominance was established more rapidly in flow channels incubated at 350 μM NH4+than in those incubated at 50 or 20 μM NH4+. Biofilm-associated potential nitrification activity was first detected after 28 days and was positively correlated with bacterial but not archaealamoAgene copy numbers.

Seasonal variation of deep soil moisture under different land uses on the semi-arid Loess Plateau of China

2018 ◽  
Vol 19 (3) ◽  
pp. 1179-1189 ◽  
Author(s):  
Bowei Yu ◽  
Gaohuan Liu ◽  
Qingsheng Liu ◽  
Chong Huang ◽  
He Li ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Seasonal Variation ◽  
Loess Plateau ◽  
Land Uses ◽  
Deep Soil ◽  
Semi Arid

scholarly journals Evaluating agronomic factors for maize production in semi‐arid Loess Plateau

2021 ◽  
Author(s):  
Gaimei Liang ◽  
Baoliang Chi ◽  
Nana Li ◽  
Wenliang Chen ◽  
Wei Qin ◽  
...  
Keyword(s):  
Loess Plateau ◽  
Maize Production ◽  
Semi Arid

scholarly journals Effects of clouds and precipitation disturbance on the surface radiation budget and energy balance over loess plateau semi-arid grassland in China

2013 ◽  
Vol 62 (20) ◽  
pp. 209201
Author(s):  
Yue Ping ◽  
Zhang Qiang ◽  
Zhao Wen ◽  
Wang Jin-Song ◽  
Wang Run-Yuan ◽  
...  
Keyword(s):  
Energy Balance ◽  
Loess Plateau ◽  
Surface Radiation ◽  
Radiation Budget ◽  
Surface Radiation Budget ◽  
Semi Arid

scholarly journals First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5963 ◽  
Author(s):  
Balázs Brankovics ◽  
Tomasz Kulik ◽  
Jakub Sawicki ◽  
Katarzyna Bilska ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Fusarium Graminearum ◽  
Population Analysis ◽  
Gene Copy ◽  
Sequence Length ◽  
Length Variation ◽  
Group I Introns ◽  
Group I ◽  
Pooled Sequencing ◽  
Mitochondrial Introns

There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.

scholarly journals The effects of clouds and aerosols on net ecosystem CO<sub>2</sub> exchange over semi-arid Loess Plateau of Northwest China

2010 ◽  
Vol 10 (5) ◽  
pp. 13337-13372
Author(s):  
X. Jing ◽  
J. Huang ◽  
G. Wang ◽  
K. Higuchi ◽  
J. Bi ◽  
...  
Keyword(s):  
Loess Plateau ◽  
Air Temperature ◽  
Northwest China ◽  
Co2 Uptake ◽  
Observation Data ◽  
Light Use Efficiency ◽  
Clearness Index ◽  
Use Efficiency ◽  
The Difference ◽  
Semi Arid

Abstract. The impacts of clouds and atmospheric aerosols on the terrestrial carbon cycle at semi-arid Loess Plateau in Northwest China are investigated, by using the observation data obtained at the SACOL (Semi-Arid Climate and Environment Observatory of Lanzhou University) site. Daytime (solar elevation angles of larger than 50°) NEE of CO2 obtained during the midgrowing season (July–August) are analyzed with respect to variations in the diffuse radiation, cloud cover and aerosol optical depth (AOD). Results show a significant impact by clouds and aerosols on the CO2 uptake by the grassland (with smaller LAI values) located in a semi-arid region, quite different from areas covered by forests and crops. The light saturation levels in canopy are lower, with a value of about 434.8 W m−2. Thus, under overcast conditions of optically thick clouds, the CO2 uptake increases with increasing clearness index, and a maximum CO2 uptake and light use efficiency of vegetation occur with the clearness index of about 0.37 and lower air temperature. Under other sky conditions the CO2 uptake decreases with the cloudiness but the light use efficiency is enhanced, due to increase in the fraction of diffuse PAR. Additionally, under cloudy conditions, changes in the NEE of CO2 also result from the interactions of many environmental factors, especially the air temperature. In contrast to its response to changes in solar radiation, the carbon uptake shows a negative response to increased AOD. The reason for the difference in the response of the semi-arid grassland from that of the forest and crop lands may be due to the difference in the canopy's architectural structure.

Sign in / Sign up

Export Citation Format

Share Document