scholarly journals Changes in Denitrification Potentials and Riverbank Soil Bacterial Structures along Shibetsu River, Japan

2018 ◽  
Vol 2018 ◽  
pp. 1-9
Author(s):  
Yoshitaka Uchida ◽  
Hirosato Mogi ◽  
Toru Hamamoto ◽  
Miwako Nagane ◽  
Misato Toda ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Inorganic Nitrogen ◽  
Anaerobic Incubation ◽  
Community Structures ◽  
Bacterial Response ◽  
Glucose Carbon ◽  
Soil Ecosystems ◽  
Increase Rate ◽  
Before And After ◽  
C And N

Riverbank soil ecosystems are important zones in terms of transforming inorganic nitrogen (N), particularly nitrate (NO3−-N), in soils to nitrous oxide (N2O) gases. Thus, the gasification of N in the riverbank soil ecosystems may produce a greenhouse gas, N2O, when the condition is favourable for N2O-producing microbes. One of the major N2O-producing pathways is denitrification. Thus, we investigated the denitrification potentials along Shibetsu River, Hokkaido, Japan. We sampled riverbank soils from eight sites along the Shibetsu River. Their denitrification potentials with added glucose-carbon (C) and NO3−-N varied from 4.73 to 181 μg·N·kg−1·h−1. The increase of the denitrification after the addition of C and N was negatively controlled by soil pH and positively controlled by soil NH4+-N levels. Then, we investigated the changes in 16S rRNA bacterial community structures before and after an anaerobic incubation with added C and N. We investigated the changes in bacterial community structures, aiming to identify specific microbial species related to high denitrification potentials. The genus Gammaproteobacteria AeromonadaceaeTolumonaswas markedly increased, from 0.0 ± 0.0% to 16 ± 17%, before and after the anaerobic incubation with the excess substrates, when averaged across all the sites. Although we could not find a significant interaction between the denitrification potential and the increase rate of G. AeromonadaceaeTolumonas, our study suggested that along the Shibetsu River, bacterial response to added excess substrates was similar at the genus level. Further studies are needed to investigate whether this is a universal phenomenon even in other rivers.

scholarly journals The effects of Hurricane Otto on the soil ecosystems of three forest types in the Northern Zone of Costa Rica

2020 ◽  
Author(s):  
William D. Eaton ◽  
Katie M. McGee ◽  
Kiley Alderfer ◽  
Angie Ramirez Jimenez ◽  
Mehrdad Hajibabaei
Keyword(s):  
Costa Rica ◽  
Tropical Forest ◽  
Soil Samples ◽  
Permanent Plots ◽  
Total N ◽  
Organic C ◽  
Soil Ecosystems ◽  
Before And After ◽  
Northern Zone ◽  
C And N

AbstractHurricanes rapidly deposit large amounts of canopy material onto tropical forest floors, stimulating metabolic processes involved in the decomposition of these materials and production of N and C resources into the food web. However, little is known about the effects that hurricanes have on specific soil microbial taxa or functional groups involved in these processes. The objectives of this study were to determine how Hurricane Otto influenced three different tropical forest soil ecosystems within the first 8 months after causing damage to a tropical forest by assessing the soil C and N factors and how the soil bacterial and fungal community compositions differed before and after the hurricane. Soil samples were collected from five 2000 m2 permanent plots in Lowland, Upland and Riparian forest systems within the same area in the Northern Zone of Costa Rica. Standard methods were used to measure the amounts Total N, NO3-, NH4+, Total organic C, and Biomass C, while Illumina MiSeq methods were used to generate bacterial and fungal sequences. All data were analyzed using univariate and multivariate statistical methods. Using this “before and after” study design, it was found that the levels of the inorganic N and Biomass C were greater in the Post-Hurricane soil samples. The mean proportion of DNA sequences of complex C degrading/lignin degrading, NH4+-producing, and ammonium oxidizing bacteria, and the complex C degrading/wood rot/lignin degrading and ectomycorrhizal fungi also were greater in the Post-Hurricane soils. We also provide evidence that the excessive amounts of canopy leaf litter and woody debris deposited on the forest floor during Hurricane Otto appears to be selecting for genera that become more dominant Post-Hurricane, perhaps because they may be better able to rapidly process the newly deposited C and N-rich canopy material. This is a rare “before and after” a natural hurricane design that warrants further monitoring.

scholarly journals Maize root and shoot litter quality controls short-term CO<sub>2</sub> and N<sub>2</sub>O emissions and bacterial community structure of arable soil

2019 ◽  
Author(s):  
Pauline Sophie Rummel ◽  
Birgit Pfeiffer ◽  
Johanna Pausch ◽  
Reinhard Well ◽  
Dominik Schneider ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Litter Quality ◽  
Plant Litter ◽  
Maize Root ◽  
N2o Emissions ◽  
Community Structures ◽  
Root Litter ◽  
C And N

Abstract. Chemical composition of root and shoot litter controls decomposition and, subsequently, C availability for biological nitrogen transformation processes in soils. While aboveground plant residues have been proven to increase N2O emissions, studies on root litter effects are scarce. This study aimed (1) to evaluate how fresh maize root litter affects N2O emissions compared to fresh maize shoot litter, (2) to assess whether N2O emissions are related to the interaction of C and N mineralization from soil and litter, and (3) to analyze changes in soil microbial community structures related to litter input and N2O emissions. To obtain root and shoot litter, Maize plants (Zea mays L.) were cultivated with two N fertilizer levels in a greenhouse and harvested. A two-factorial 22-day laboratory incubation experiment was set up with soil from both N levels (N1, N2) and three litter addition treatments (Control, Root, Root+Shoot). We measured hourly CO2 and N2O fluxes, analyzed soil nitrate and water extractable organic C (WEOC) concentrations, and determined quality parameters of maize litter. Bacterial community structures were analyzed using 16S rRNA gene sequencing. Maize litter quality controlled NO3− and WEOC availability and decomposition related CO2 emissions. High bioavailability of maize shoot litter strongly increased CO2 and N2O emissions, while emissions induced by maize root litter remained low. We identified a strong positive correlation between cumulative CO2 and N2O emissions, supporting our hypothesis that litter quality affects denitrification by creating plant litter associated anaerobic microsites. The interdependency of C and N availability was validated by analyses of regression. Moreover, there was a strong positive interaction between soil NO3− and WEOC concentration resulting in much higher N2O emissions, when both NO3− and WEOC were available. A significant correlation was observed between total CO2 and N2O emissions, the soil bacterial community composition and the litter level, showing a clear separation of Root+Shoot samples of all remaining samples. Bacterial diversity decreased with higher N level and higher input of easily available C. Altogether, changes in bacterial community structure reflected degradability of maize litter with easily degradable C from maize shoot litter favoring fast growing C cycling and N reducing bacteria of the phyla Actinobacteria, Chloroflexi, Firmicutes and Proteobacteria.

scholarly journals Microbial Population Changes during Bioremediation of an Experimental Oil Spill

1999 ◽  
Vol 65 (8) ◽  
pp. 3566-3574 ◽  
Author(s):  
Sarah J. MacNaughton ◽  
John R. Stephen ◽  
Albert D. Venosa ◽  
Gregory A. Davis ◽  
Yun-Juan Chang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Oil Spill ◽  
Phospholipid Fatty Acid ◽  
Community Structures ◽  
Gram Negative ◽  
Dgge Analysis ◽  
16S Rdna Pcr ◽  
Microbial Community Structures ◽  
Plfa Analysis

ABSTRACT Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria andFlexibacter-Cytophaga-Bacteroides phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained.

Bacterioplankton, Phytoplankton, and Zooplankton Communities in a British Columbia Coastal Lake Before and After Nutrient Reduction

1986 ◽  
Vol 43 (8) ◽  
pp. 1504-1514 ◽  
Author(s):  
F. Joan Hardy ◽  
Ken S. Shortreed ◽  
John G. Stockner
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Inorganic Nitrogen ◽  
Size Fraction ◽  
Growing Season ◽  
Nutrient Reduction ◽  
Nitrogen And Phosphorus ◽  
Coastal Lake ◽  
Before And After ◽  
High Concentrations

Inorganic nitrogen and phosphorus were applied weekly during the growing season from 1980 to 1982 and twice weekly in 1983 to Hobiton Lake, a warm monomictic coastal lake in British Columbia. The lake was not fertilized in 1984. Average numbers of bacteria during the growing season decreased from a high of 1.53 × 106∙mL−1 in the fertilized condition to 0.84 × 106∙mL−1 in the unfertilized condition. Chlorophyll a concentrations decreased from a maximum seasonal average of 2.69 μg∙L−1 (1981) to 1.30 μg∙L−1 (1984), and algal numbers decreased from 5.83 × 104∙mL−1 (1983) to 2.29 × 104∙mL−1 (1984). Although the numbers of phytoplankton in each size fraction (picoplankton, nanoplankton, or microplankton) decreased in the unfertilized condition, the greatest change was an almost fourfold decrease in picoplankton, which consisted of 90% cyanobacteria (primarily Synechococcus spp.). Abundance of the large diatoms Rhizosolenia spp. and Melosira spp. increased in 1984, resulting in an increase in average seasonal algal volume. Average densities of medium (0.15–0.84 mm) and large (0.85–1.5 mm) zooplankton were greatest in 1982, while rotifers and small zooplankton (0.10–0.14 mm) were most dense in 1984 following nutrient reduction. The lake had relatively high concentrations of planktivorous juvenile sockeye salmon (Oncorhynchus nerka) that appeared to minimize any direct effect of nutrient additions on zooplankton densities.

scholarly journals Bacterial community structures are unique and resilient in full-scale bioenergy systems

2011 ◽  
Vol 108 (10) ◽  
pp. 4158-4163 ◽  
Author(s):  
J. J. Werner ◽  
D. Knights ◽  
M. L. Garcia ◽  
N. B. Scalfone ◽  
S. Smith ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Full Scale ◽  
Community Structures ◽  
Bioenergy Systems

Analyses of Aerosol Concentrations and Bacterial Community Structures for Closed Cage Broiler Houses at Different Broiler Growth Stages in Winter

2018 ◽  
Vol 81 (9) ◽  
pp. 1557-1564
Author(s):  
LINLIN JIANG ◽  
JIANLONG ZHANG ◽  
JINXIU TANG ◽  
MENG LI ◽  
XIAOYU ZHAO ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Total Concentration ◽  
Growth Period ◽  
Growth Cycle ◽  
Growth Stages ◽  
Community Structures ◽  
Dynamic Pattern ◽  
Different Growth Stages

ABSTRACT The aim of the present study was to analyze the aerosol concentrations and microbial community structures in closed cage broiler houses at different broiler growth stages to assess the dynamic pattern of microbial aerosols in closed cage systems. Our results revealed that the total concentration of bacterial aerosols gradually increased during the growth cycle of broilers. High-throughput sequencing of 16S rDNA revealed that microbial compositions differed tremendously during different growth stages, although Firmicutes and Proteobacteria were the dominant taxa in samples from all broiler growth stages. At the genus level, dominant phylotypes displayed great variation during different growth stages. Escherichia and Shigella were the most dominant taxa throughout the growth cycle, increasing from 4.3 to 12.4% as the broilers grew. The alpha index revealed that the microbial diversity displayed significant differences between the different growth stages and that the bacterial community had the highest diversity when broilers were 22 days old. High-throughput sequencing analyses revealed that environmental microbes and opportunistic pathogens had relatively high abundances during the winter growth period. The data revealed the composition and aerodynamic diameters of microbial aerosols in closed cage broiler houses at different broiler growth stages in winter. The results also enabled us to elucidate the dynamic pattern of microbial aerosols in broiler houses in response to bacterial communities. Our results may provide a basis for developing technologies for air quality control in caged poultry houses.

A decade of land use contributes to changes in the chemistry, biochemistry and bacterial community structures of soils in the Cerrado

2010 ◽  
Vol 98 (3) ◽  
pp. 403-413 ◽  
Author(s):  
R. S. Peixoto ◽  
G. M. Chaer ◽  
N. Franco ◽  
F. B. Reis Junior ◽  
I. C. Mendes ◽  
...  
Keyword(s):  
Land Use ◽  
Bacterial Community ◽  
Community Structures
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