scholarly journals Higher Sensitivity of Soil Microbial Network Than Community Structure under Acid Rain

2021 ◽  
Vol 9 (1) ◽  
pp. 118
Author(s):  
Ziqiang Liu ◽  
Hui Wei ◽  
Jiaen Zhang ◽  
Muhammad Saleem ◽  
Yanan He ◽  
...  
Keyword(s):  
Community Structure ◽  
Acid Rain ◽  
Natural Soil ◽  
Available Phosphorus ◽  
Global Changes ◽  
N2o Emissions ◽  
Ammonia Oxidizing Bacteria ◽  
Soil Core ◽  
N Cycle ◽  
Microbial Network

Acid rain (AR), as a global environmental threat, has profoundly adverse effects on natural soil ecosystems. Microorganisms involved in the nitrogen (N) cycle regulate the global N balance and climate stabilization, but little is known whether and how AR influences the structure and complexity of these microbial communities. Herein, we conducted an intact soil core experiment by manipulating the acidity of simulated rain (pH 7.5 (control, CK) vs. pH 4.0 (AR)) in subtropical agricultural soil, to reveal the differences in the structure and complexity of soil nitrifying and denitrifying microbiota using Illumina amplicon sequencing of functional genes (amoA, nirS, and nosZ). Networks of ammonia-oxidizing archaea (AOA) and nirS-carrying denitrifiers in AR treatment were less complex with fewer nodes and lower connectivity, while network of nosZ-carrying denitrifiers in AR treatment had higher complexity and connectivity relative to CK. Supporting this, AR reduced the abundance of keystone taxa in networks of AOA and nirS-carrying denitrifiers, but increased the abundance of keystone taxa in nosZ-carrying denitrifiers network. However, AR did not alter the community structure of AOA, ammonia-oxidizing bacteria (AOB), nirS-, and nosZ-carrying denitrifiers. Moreover, AR did not change soil N2O emissions during the experimental period. AOB community structure significantly correlated with content of soil available phosphorus (P), while the community structures of nirS- and nosZ-carrying denitrifiers both correlated with soil pH and available P content. Soil N2O emission was mainly driven by the nirS-carrying denitrifiers. Our results present new perspective on the impacts of AR on soil N-cycle microbial network complexity and keystone taxa in the context of global changes.

scholarly journals Effects of Organic Fertilizers on the Soil Microorganisms Responsible for N2O Emissions: A Review

2021 ◽  
Vol 9 (5) ◽  
pp. 983
Author(s):  
Cristina Lazcano ◽  
Xia Zhu-Barker ◽  
Charlotte Decock
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Best Management Practices ◽  
Management Practices ◽  
Organic Fertilizers ◽  
N2o Emissions ◽  
Soil C ◽  
Best Management ◽  
C Stocks ◽  
Denitrifying Microorganisms

The use of organic fertilizers constitutes a sustainable strategy to recycle nutrients, increase soil carbon (C) stocks and mitigate climate change. Yet, this depends largely on balance between soil C sequestration and the emissions of the potent greenhouse gas nitrous oxide (N2O). Organic fertilizers strongly influence the microbial processes leading to the release of N2O. The magnitude and pattern of N2O emissions are different from the emissions observed from inorganic fertilizers and difficult to predict, which hinders developing best management practices specific to organic fertilizers. Currently, we lack a comprehensive evaluation of the effects of OFs on the function and structure of the N cycling microbial communities. Focusing on animal manures, here we provide an overview of the effects of these organic fertilizers on the community structure and function of nitrifying and denitrifying microorganisms in upland soils. Unprocessed manure with high moisture, high available nitrogen (N) and C content can shift the structure of the microbial community, increasing the abundance and activity of nitrifying and denitrifying microorganisms. Processed manure, such as digestate, compost, vermicompost and biochar, can also stimulate nitrifying and denitrifying microorganisms, although the effects on the soil microbial community structure are different, and N2O emissions are comparatively lower than raw manure. We propose a framework of best management practices to minimize the negative environmental impacts of organic fertilizers and maximize their benefits in improving soil health and sustaining food production systems. Long-term application of composted manure and the buildup of soil C stocks may contribute to N retention as microbial or stabilized organic N in the soil while increasing the abundance of denitrifying microorganisms and thus reduce the emissions of N2O by favoring the completion of denitrification to produce dinitrogen gas. Future research using multi-omics approaches can be used to establish key biochemical pathways and microbial taxa responsible for N2O production under organic fertilization.

scholarly journals Vertical distribution of soil available phosphorus and soil available potassium in the critical zone on the Loess Plateau, China

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hanyang Tian ◽  
Jiangbo Qiao ◽  
Yuanjun Zhu ◽  
Xiaoxu Jia ◽  
Ming’an Shao
Keyword(s):  
Vertical Distribution ◽  
Loess Plateau ◽  
Clay Content ◽  
Exponential Model ◽  
Critical Zone ◽  
Available Phosphorus ◽  
Soil Core ◽  
The Loess Plateau ◽  
Deep Soil ◽  
Soil Available Phosphorus

AbstractSoil available phosphorus (SAP) and soil available potassium (SAK) are important elements in the growth of plants. However, limited data are available regarding the vertical distribution of SAP and SAK in deep soil profiles. In this study, we investigated the vertical variations in SAP and SAK in the critical zone on the Loess Plateau (50–200 m), China, by using classical statistical and geostatistical methods. The soil samples were collected from the top of the soil profile down to the bedrock by soil core drilling at five typical sites. SAP decreased throughout the profile. Whereas the SAK exhibited an increasing trend at all sites. The mean SAP concentration ranged from 0.94 to 32.56 mg kg–1 at the sampling sites and the SAK concentration ranged from 44.51 to 229.31 mg kg–1. At all of the sampling sites, SAK was significantly positively correlated with the depth and clay content, but there was a significantly negative correlation between the SAK and the sand content. The exponential model could fit most variograms of SAP and SAK at all sampling sites. The results obtained in this study to improve our comprehension of the SAP or SAK distribution conditions on the Loess Plateau, which is important for reasonable fertilizer application and vegetation planting practices.

scholarly journals Soil type determines the abundance and community structure of ammonia-oxidizing bacteria and archaea in flooded paddy soils

2010 ◽  
Vol 10 (8) ◽  
pp. 1510-1516 ◽  
Author(s):  
Xin Chen ◽  
Li-Mei Zhang ◽  
Ju-Pei Shen ◽  
Zhihong Xu ◽  
Ji-Zheng He
Keyword(s):  
Community Structure ◽  
Soil Type ◽  
Paddy Soils ◽  
Ammonia Oxidizing Bacteria

scholarly journals Impact of Body Mass Index (BMI) on the Effect of a Lactobacillus Rhamnosus GG (LGG)/Bifidobacterium Animalis Subspecies Lactis BB-12 (BB-12) Combination on Gut Microbiota (P20-023-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Debra Poutsiaka ◽  
Lori Stern ◽  
Virginia Riquelme ◽  
Emily Hollister ◽  
Julia Cope ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Lactobacillus Rhamnosus ◽  
Detailed Examination ◽  
Global Changes ◽  
Shotgun Metagenomics ◽  
Gene Abundance ◽  
Funding Sources ◽  
And Function ◽  
Relative Gene

Abstract Objectives This exploratory study builds upon an earlier study of probiotic supplementation1 to assess the effects of a probiotic combination (P) of LGG and BB-12 on human gut microbiota composition and function, and to uncover an association with BMI. Methods Healthy subjects ingested P for 21 days (n = 18, P group) or did not (n = 7, C group). Fecal samples obtained at baseline (D_0) and after 21 days of supplementation (D_21) underwent 16S ribosomal RNA gene and shotgun metagenomics sequencing to characterize the bacterial and archaeal communities to the genus/species level and identify functional community genes. Results Following P ingestion, no global differences in microbiota community structure or relative gene abundance were detected. In targeted analyses, the abundances of LGG and BB-12 in the P group at D_21 increased in a statistically significant manner as the BMI decreased (Spearman correlation, P = 0.04 and P = 0.01, respectively). The relative abundance of LGG but not BB-12 appeared increased in P subjects at D_21 with BMI < 25 compared to BMI > 25 (P = 0.09). P group subjects with BMI < 25 demonstrated trends toward or statistically significant increases in the relative abundances of 5 genes involved with flagellar structure (KEGG orthologs K02422, P = 0.04; K03406, P = 0.06; K02407, P = 0.08; K02397, P = 0.08; K02396, P = 0.09) at D_21 compared to those with BMI > 25. No such differences were observed for the C group nor were there differences in relative gene abundance at D_0 in the P group with BMI < 25 vs BMI > 25. Conclusions We observed no global changes in the fecal microbial community structure or function with P ingestion in this sample of healthy persons. However, we did observe patterns suggestive of a potential link between BMI and the response of the gut microbiota to P. Although our results are based on a small number of subjects, they are in line with previous findings related to LGG supplementation and the expression of flagellar genes2. We agree with other recent reports that future studies would benefit from a detailed examination of the transcriptome, proteome and/or metabolome to better understand the potential impact of probiotics on the gut microbiota, and the mechanism of the effect of BMI. Funding Sources Pfizer Inc.

scholarly journals The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function

2003 ◽  
Vol 69 (11) ◽  
pp. 6875-6887 ◽  
Author(s):  
Justyna Adamczyk ◽  
Martin Hesselsoe ◽  
Niels Iversen ◽  
Matthias Horn ◽  
Angelika Lehner ◽  
...  
Keyword(s):  
Community Structure ◽  
Activated Sludge ◽  
Fluorescence Labeling ◽  
Specific Substrate ◽  
Ammonia Oxidizing Bacteria ◽  
Microarray Hybridization ◽  
Independent Manner ◽  
And Function

ABSTRACT A new microarray method, the isotope array approach, for identifying microorganisms which consume a 14C-labeled substrate within complex microbial communities was developed. Experiments were performed with a small microarray consisting of oligonucleotide probes targeting the 16S rRNA of ammonia-oxidizing bacteria (AOB). Total RNA was extracted from a pure culture of Nitrosomonas eutropha grown in the presence of [14C]bicarbonate. After fluorescence labeling of the RNA and microarray hybridization, scanning of all probe spots for fluorescence and radioactivity revealed that specific signals were obtained and that the incorporation of 14C into rRNA could be detected unambiguously. Subsequently, we were able to demonstrate the suitability of the isotope array approach for monitoring community composition and CO2 fixation activity of AOB in two nitrifying activated-sludge samples which were incubated with [14C]bicarbonate for up to 26 h. AOB community structure in the activated-sludge samples, as predicted by the microarray hybridization pattern, was confirmed by quantitative fluorescence in situ hybridization (FISH) and comparative amoA sequence analyses. CO2 fixation activities of the AOB populations within the complex activated-sludge communities were detectable on the microarray by 14C incorporation and were confirmed independently by combining FISH and microautoradiography. AOB rRNA from activated sludge incubated with radioactive bicarbonate in the presence of allylthiourea as an inhibitor of AOB activity showed no incorporation of 14C and thus was not detectable on the radioactivity scans of the microarray. These results suggest that the isotope array can be used in a PCR-independent manner to exploit the high parallelism and discriminatory power of microarrays for the direct identification of microorganisms which consume a specific substrate in the environment.

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