scholarly journals Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil

Archaea ◽  
2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Yendi E. Navarro-Noya ◽  
César Valenzuela-Encinas ◽  
Alonso Sandoval-Yuriar ◽  
Norma G. Jiménez-Bueno ◽  
Rodolfo Marsch ◽  
...  
Keyword(s):  
Species Richness ◽  
Alpha Diversity ◽  
Methanogenic Archaea ◽  
Archaeal Community ◽  
Soil Samples ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Phylogenetic Information ◽  
Archaeal Communities ◽  
Saline Alkaline Soils

In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic CandidatusNitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils.Halobiforma,Halostagnicola,Haloterrigena, andNatronomonaswere found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH.

scholarly journals The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2139
Author(s):  
Feilong Deng ◽  
Yushan Li ◽  
Yunjuan Peng ◽  
Xiaoyuan Wei ◽  
Xiaofan Wang ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Antibiotic Resistance Genes ◽  
Alpha Diversity ◽  
Distance Matrix ◽  
Archaeal Community ◽  
Gene Families ◽  
Shannon Index ◽  
Metabolic Potential ◽  
Substantial Progress ◽  
Archaeal Communities

Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray–Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

scholarly journals The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs

2021 ◽  
Author(s):  
Feilong Deng ◽  
Yushan Li ◽  
Xiaoyuan Wei ◽  
Xiaofan Wang ◽  
Samantha Howe ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Antibiotic Resistance Genes ◽  
Alpha Diversity ◽  
Distance Matrix ◽  
Archaeal Community ◽  
Gene Families ◽  
Shannon Index ◽  
Metabolic Potential ◽  
Substantial Progress ◽  
Archaeal Communities

Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n=76), Denmark (n=100), and France (n=100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (P&lt;0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus Methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus Methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32%, 11.67%, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being: AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

scholarly journals Laboratory Research on Polarized Optical Properties of Saline-Alkaline Soil Based on Semi-Empirical Models and Machine Learning Methods

2022 ◽  
Vol 14 (1) ◽  
pp. 226
Author(s):  
Qianyi Gu ◽  
Yang Han ◽  
Yaping Xu ◽  
Haiyan Yao ◽  
Haofang Niu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Empirical Models ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Model Based ◽  
Semi Empirical ◽  
Saline Alkaline Soils

Currently, soil salinization is a serious problem affecting agricultural production and human settlements. Remote sensing techniques have the advantages of a large monitoring range, rapid acquisition of information, implementation of dynamic monitoring, and low impact on the ground surface. Over the past two decades, many semi-empirical bidirectional polarized distribution function (BPDF) models have been proposed to accurately calculate the polarized reflectance (Rp) on the soil surface. Although there have been some studies on the BPDF model based on traditional machine learning methods, there is a lack of research on the BPDF model based on deep learning, especially using laboratory measurement spectrum data as the processing object, with limited research results. In this paper, we collected saline-alkaline soil in the field as the observation object and measured the Rp at multiple angles in the laboratory environment. We used semi-empirical models (the Nadal–Bréon model, Litvinov model, and Xie–Cheng model) and machine learning methods (support vector regression, random forest, and deep neural networks regression) to simulate and predict the surface Rp of saline-alkaline soils and compare them with experimental results. The measured values of the laboratory are compared and fitted, and the root mean squared error, R-squared, and correlation coefficient are calculated to express the prediction effect. The results show that the predictions of the BPDF model based on machine learning methods are generally better than those of the semi-empirical BPDF model, which is improved by 3.06% at 670 nm and 19.75% at 865 nm. The results of this study also provide new ideas and methods based on deep learning for the prediction of Rp on the surface of saline-alkaline soils.

scholarly journals Silicon Improves Maize Photosynthesis in Saline-Alkaline Soils

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Zhiming Xie ◽  
Ri Song ◽  
Hongbo Shao ◽  
Fengbin Song ◽  
Hongwen Xu ◽  
...  
Keyword(s):  
Photosynthetic Efficiency ◽  
Optimal Dose ◽  
Growth And Yield ◽  
Growth Stages ◽  
Alkaline Stress ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Saline Alkaline Soils ◽  
Different Growth Stages ◽  
Maize Photosynthesis

The research aimed to determine the effects of Si application on photosynthetic characteristics of maize on saline-alkaline soil, including photosynthetic rate (Pn), stomatal conductance (gs), transpiration rate (E), and intercellular CO2concentration (Ci) of maize in the field with five levels (0, 45, 90, 150, and 225 kg·ha−1) of Si supplying. Experimental results showed that the values ofPn,gs, andCiof maize were significantly enhanced while the values ofEof maize were dramatically decreased by certain doses of silicon fertilizers, which meant that Si application with proper doses significantly increased photosynthetic efficiency of maize in different growth stages under stressing environment of saline-alkaline soil. The optimal dose of Si application in this experiment was 150 kg·ha−1 Si. It indicated that increase in maize photosynthesis under saline-alkaline stress took place by Si application with proper doses, which is helpful to improve growth and yield of maize.

scholarly journals Trichoderma asperellum improves soil microenvironment in different growth stages and yield of maize in saline-alkaline soil of the Songnen Plain

2020 ◽  
Vol 66 (No. 12) ◽  
pp. 639-647
Author(s):  
Jian Fu ◽  
Yao Xiao ◽  
Zhihua Liu ◽  
Yifei Zhang ◽  
Yufeng Wang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Nutrients ◽  
Crop Yield ◽  
Alkaline Soil ◽  
Trichoderma Asperellum ◽  
Alkaline Soils ◽  
Songnen Plain ◽  
Cold Region ◽  
Maize Rhizosphere ◽  
Saline Alkaline Soils

The Songnen Plain is an important agricultural base in China and one of the important areas of distribution of saline-alkaline soils in the cold region. Saline-alkaline soils severely restrict maize growth. This study was to potentially promote the soil nutrient in the maize rhizosphere, microbes diversity, and maize yield by Trichoderma asperellum in saline-alkaline soil of the cold region. In the present study, we applied different amounts of T. asperellum in field experiments for three consecutive years. High-throughput sequencing was used to analyse the impact of Trichoderma on microbes diversity in maize rhizosphere soils. Changes in crop yield and soil nutrients were also monitored. T. asperellum treatment significantly increased the relative abundance of beneficial microbes genera. In the control treatment, the pathogenic microbes were the dominant genera. Pearson’s correlation analysis revealed that changes in the soil microbial community composition were closely related to soil nutrients and were highly correlated with T. asperellum treatment concentration. Further, T. asperellum treatment increased crop yield by 4.87–20.26%. These findings suggest that T. asperellum treatment optimised the microenvironment of the maize rhizosphere soil, alleviated microbial community degeneration in cold region saline-alkaline soil, and promoted maize growth.  

scholarly journals The diversity, composition, and metabolic pathways of archaea in pigs

2021 ◽  
Author(s):  
Feilong Deng ◽  
Yushan Li ◽  
Xiaoyuan Wei ◽  
Yingping Xiao ◽  
Xiaofan Wang ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Antibiotic Resistance Genes ◽  
Alpha Diversity ◽  
Distance Matrix ◽  
Archaeal Community ◽  
Gene Families ◽  
Shannon Index ◽  
Metabolic Potential ◽  
Substantial Progress ◽  
Archaeal Communities

Abstract Background Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. To this end, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset from the NCBI Sequence Read Archive (SRA) database. Results A total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100) were used in this study. For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (P < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus Methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus Methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32%, 11.67%, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being: AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Conclusions Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Lucas Dantas Lopes ◽  
Jingjie Hao ◽  
Daniel P Schachtman
Keyword(s):  
Microbial Communities ◽  
Plant Species ◽  
Soil Ph ◽  
Soil Microbial Communities ◽  
Bulk Soil ◽  
Strong Impact ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Soil Microbial ◽  
Soil Rhizosphere

ABSTRACT Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.

scholarly journals Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean

Archaea ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Franziska Wemheuer ◽  
Avril Jean Elisabeth von Hoyningen-Huene ◽  
Marion Pohlner ◽  
Julius Degenhardt ◽  
Bert Engelen ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Primary Production ◽  
Deep Sea ◽  
Archaeal Community ◽  
Central Pacific ◽  
Central Pacific Ocean ◽  
Deep Sea Sediments ◽  
And Function ◽  
Functional Profiles ◽  
Archaeal Communities

Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean. Community composition and diversity were assessed by Illumina tag sequencing targeting archaeal 16S rRNA genes and transcripts. Archaeal communities were dominated by CandidatusNitrosopumilus(Thaumarchaeota) and other members of theNitrosopumilaceae(Thaumarchaeota), but higher relative abundances of the Marine Group II (Euryarchaeota) were observed in the active compared to the entire archaeal community. The composition of the entire and the active archaeal communities was strongly linked to primary production (chlorophyll content), explaining more than 40% of the variance. Furthermore, we found a strong correlation of the entire archaeal community composition to latitude and silicic acid content, while the active community was significantly correlated with primary production and ferric oxide content. We predicted functional profiles from 16S rRNA data to assess archaeal community functions. Latitude was significantly correlated with functional profiles of the entire community, whereas those of the active community were significantly correlated with nitrate and chlorophyll content. The results of the present study provide first insights into benthic archaeal communities in the Pacific Ocean and environmental conditions shaping their diversity, distribution, and function. Additionally, they might serve as a template for further studies investigating archaea colonizing deep-sea sediments.

scholarly journals Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses

Archaea ◽  
2005 ◽  
Vol 1 (6) ◽  
pp. 391-397 ◽  
Author(s):  
Atsuo Sugano ◽  
Hidetaka Tsuchimoto ◽  
Tun Cho Cho ◽  
Makoto Kimura ◽  
Susumu Asakawa
Keyword(s):  
Rice Straw ◽  
Rice Field ◽  
Previous History ◽  
Methanogenic Archaea ◽  
Leaf Sheath ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Crop Season ◽  
Rdna Sequencing ◽  
Archaeal Communities

The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related toMethanomicrobialesand Rice cluster I.Methanomicrobiales, Rice cluster I andMethanosarcinaleswere major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related toMethanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade) and the previous history of decomposition during the off-crop season.

Preferential nitrate immobilization in alkaline soils

Soil Research ◽  
1992 ◽  
Vol 30 (5) ◽  
pp. 737 ◽  
Author(s):  
IJ Rochester ◽  
GA Constable ◽  
DA Macleod
Keyword(s):  
Acid Soil ◽  
Nitrification Inhibitor ◽  
Biological Significance ◽  
Nitrate Assimilation ◽  
Acid Soils ◽  
Ammonium Assimilation ◽  
Potassium Nitrate ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Nitrate Immobilization

The literature pertaining to N immobilization indicates that ammonium is immobilized in preference to nitrate. Our previous research in an alkaline clay soil has indicated substantial immobilization of nitrate. To verify the preference for immobilization of nitrate or ammonium by the microbial biomass in this and other soil types, the immobilization of ammonium and nitrate from applications of ammonium sulfate and potassium nitrate following the addition of cotton crop stubble was monitored in six soils. The preference for ammonium or nitrate immobilization was highly correlated with each soil's pH, C/N ratio and its nitrification capacity. Nitrate was immobilized in preference to ammonium in neutral and alkaline soils; ammonium was preferentially immobilized in acid soils. No assimilation of nitrate (or nitrification) occurred in the most acid soil. Similarly, little assimilation of ammonium occurred in the most alkaline soil. Two physiological pathways, the nitrate assimilation pathway and the ammonium assimilation pathway, appear to operate concurrently; the dominance of one pathway over the other is indicated by soil pH. The addition of a nitrification inhibitor to an alkaline soil enhanced the immobilization of ammonium. Recovery of 15N confirmed that N was not denitrified, but was biologically immobilized. The immobilization of 1 5 ~ and the apparent immobilization of N were similar in magnitude. The identification of preferential nitrate immobilization has profound biological significance for the cycling of N in alkaline soils.

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