scholarly journals Structure, Assembly, and Co-Occurrence of Archaeal Communities in Tree Rhizosphere of the Qinghai-Tibetan Plateau

2020 ◽  
Author(s):  
Mengjun Zhang ◽  
Liwei Chai ◽  
Muke Huang ◽  
Weiqian Jia ◽  
Jiabao Guo ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Keystone Species ◽  
Archaeal Community ◽  
Ammonium Nitrogen ◽  
Bulk Soil ◽  
Available Phosphorus ◽  
Deterministic Processes ◽  
Occurrence Patterns ◽  
Structure Assembly ◽  
Archaeal Communities

Abstract Background: Archaea are considered to be an important component of complex microbiomes, which play vital roles in mediating soil biogeochemical processes. However, little is known about the ecology of archaeal communities in the rhizosphere, especially regarding their assembly and co-occurrence patterns. Results: Here, we used high-throughput Illumina sequencing to investigate the community variations of archaea between the rhizosphere and bulk soil collected from two native alpine tree species of the Qinghai-Tibetan Plateau. Thaumarchaeota was the dominant archaeal phylum in all soils tested, while archaeal community structures in the rhizosphere significantly differed from that in the bulk soil. Soil ammonium nitrogen, soil organic matter, available phosphorus and pH were significantly correlated with the archaeal community structure, and the deterministic processes dominated the assembly of archaeal communities across all soils. In addition, the network structures of the archaeal community in the rhizosphere were less complex than they were in the bulk soil, and an unclassified archaeal group (Unclassified_k_norank) was identified as the keystone species in all archaeal networks. Conclusions: Collectively, our findings suggest the structural variability, assembly processes, and co-occurrence patterns of archaeal communities in the rhizosphere of the the Qinghai-Tibetan Plateau, which further deepens our ecological understanding of the archaeal microbiome.

scholarly journals Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan Plateau

2020 ◽  
Author(s):  
Mengjun Zhang ◽  
Liwei Chai ◽  
Muke Huang ◽  
Weiqian Jia ◽  
Jiabao Guo ◽  
...  
Keyword(s):  
Community Structure ◽  
Tibetan Plateau ◽  
Keystone Species ◽  
Terrestrial Ecosystem ◽  
Archaeal Community ◽  
Ammonium Nitrogen ◽  
Bulk Soil ◽  
Available Phosphorus ◽  
Picea Crassifolia ◽  
Archaeal Communities

Abstract Background: The Qinghai-Tibetan Plateau represents one of the most important component of the terrestrial ecosystem and a particularly vulnerable region, which harbouring complex and diverse microbiota. The knowledge about their underground microorganisms have largely been studied, but the characteristics of rhizosphere microbiota, particularly archaeal communities remains unclear. Results: High-throughput Illumina sequencing was used to investigate the rhizosphere archaeal communities of two native alpine trees (Picea crassifolia and Populus szechuanica) living on the Qinghai-Tibetan Plateau. The archaeal community structure in rhizospheres significantly differed from that in bulk soil. Thaumarchaeota was the dominant archaeal phylum in all soils tested (92.46-98.01%), while its relative abundance in rhizospheres were significantly higher than that in bulk soil. Ammonium nitrogen, soil organic matter, available phosphorus and pH were significantly correlated with the archaeal community structure, and the deterministic processes dominated the assembly of archaeal communities across all soils. In addition, the network structures of the archaeal community in the rhizosphere were less complex than they were in the bulk soil, and an unclassified archaeal group (Unclassified_k_norank) was identified as the keystone species in all archaeal networks. Conclusions: Overall, the structure, assembly and co-occurrence patterns of archaeal communities are significantly affected by the presence of roots of alpine trees living on the Qinghai-Tibetan Plateau. This study provides new insights into our understanding of archaeal communities in vulnerable ecosystems.

scholarly journals Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan Plateau

2020 ◽  
Author(s):  
Mengjun Zhang ◽  
Liwei Chai ◽  
Muke Huang ◽  
Weiqian Jia ◽  
Jiabao Guo ◽  
...  
Keyword(s):  
Community Structure ◽  
Tibetan Plateau ◽  
Keystone Species ◽  
Terrestrial Ecosystem ◽  
Archaeal Community ◽  
Ammonium Nitrogen ◽  
Bulk Soil ◽  
Available Phosphorus ◽  
Picea Crassifolia ◽  
Archaeal Communities

Abstract Background: The Qinghai-Tibetan Plateau represents one of the most important component of the terrestrial ecosystem and a particularly vulnerable region, which harbouring complex and diverse microbiota. The knowledge about their underground microorganisms have largely been studied, but the characteristics of rhizosphere microbiota, particularly archaeal communities remains unclear.Results: High-throughput Illumina sequencing was used to investigate the rhizosphere archaeal communities of two native alpine trees (Picea crassifolia and Populus szechuanica) living on the Qinghai-Tibetan Plateau. The archaeal community structure in rhizospheres significantly differed from that in bulk soil. Thaumarchaeota was the dominant archaeal phylum in all soils tested (92.46-98.01%), while its relative abundance in rhizospheres were significantly higher than that in bulk soil. Ammonium nitrogen, soil organic matter, available phosphorus and pH were significantly correlated with the archaeal community structure, and the deterministic processes dominated the assembly of archaeal communities across all soils. In addition, the network structures of the archaeal community in the rhizosphere were less complex than they were in the bulk soil, and an unclassified archaeal group (Unclassified_k_norank) was identified as the keystone species in all archaeal networks. Conclusions: Overall, the structure, assembly and co-occurrence patterns of archaeal communities are significantly affected by the presence of roots of alpine trees living on the Qinghai-Tibetan Plateau. This study provides new insights into our understanding of archaeal communities in vulnerable ecosystems.

scholarly journals Increasing inundation frequencies enhance the stochastic process and network complexity of soil archaeal community in coastal wetlands

2021 ◽  
Author(s):  
Gui-Feng Gao ◽  
Dan Peng ◽  
Di Wu ◽  
Yihui Zhang ◽  
Haiyan Chu
Keyword(s):  
Stochastic Processes ◽  
Community Assembly ◽  
Coastal Wetlands ◽  
Southern China ◽  
Archaeal Community ◽  
Special Focus ◽  
Inundation Frequency ◽  
Occurrence Patterns ◽  
Archaeal Communities

Coastal wetlands are experiencing frequent flooding because of global climate changes, such as the rising sea level. Despite the key role of archaea in soil biogeochemical cycles, the assembly processes and co-occurrence patterns of archaeal communities in coastal wetlands in response to increasing inundation frequencies remain elusive. Herein, we established an in situ mesocosm with an inundation frequency gradient to investigate the response of soil archaeal community toward increasing inundation frequencies in monocultures of Spartina alterniflora (SA) and a mangrove species, Kandelia obovata (KO). Both neutral community model and null model analyses suggested that stochastic processes are dominant in governing the archaeal community assembly, and that the stochastic processes are enhanced with increasing inundation frequencies. Increasing inundation frequencies significantly increased the community niche width. Moreover, archaeal community in SA soil displayed lower niche overlap and higher stochasticity than in KO soil. Co-occurrence network analysis revealed that the network complexity increases with increase in the inundation frequencies. Soil water content is the most decisive factor influencing the archaeal communities. Overall, we found that increasing inundation frequencies enhance the stochastic processes and network complexity of the soil archaeal community in coastal wetlands. This study could enhance our understanding on the response of soil archaeal communities in coastal wetlands toward global change. Importance Coastal wetlands, subjected to regular disturbances by periodic tidal, are highly productive and important in the regulation of climate change. However, the assembly mechanisms and co-occurrence patterns of soil archaeal communities in coastal areas remain poorly known, especially for their responses to increasing inundation frequencies. In this study, we aim at unravelling these uncertainties by studying typical estuarine ecosystems in southern China. We show that increasing inundation frequencies enhance the stochastic processes and network complexity of the soil archaeal community. This study offers a new path for an improved understanding of archaeal community assembly and species coexistence in coastal environments, with a special focus on the role of inundation frequency.

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 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 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 keystone species of Precambrian deep bedrock biosphere belong to <i>Burkholderiales</i> and <i>Clostridiales</i>

2015 ◽  
Vol 12 (21) ◽  
pp. 18103-18150 ◽  
Author(s):  
L. Purkamo ◽  
M. Bomberg ◽  
R. Kietäväinen ◽  
H. Salavirta ◽  
M. Nyyssönen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Carbon Fixation ◽  
Keystone Species ◽  
Carbon Assimilation ◽  
Sugar Metabolism ◽  
Archaeal Community ◽  
Amino Sugar ◽  
Amplicon Sequencing ◽  
Fracture Zones ◽  
Crystalline Bedrock

Abstract. The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from six fracture zones from 180–2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related OTUs form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteraceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed the keystone genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found from oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found from other deep Precambrian terrestrial bedrock environments.

Temporal distribution of the archaeal community in the Changjiang Estuary hypoxia area and the adjacent East China Sea as determined by denaturing gradient gel electrophoresis and multivariate analysis

2011 ◽  
Vol 57 (6) ◽  
pp. 504-513 ◽  
Author(s):  
Min Liu ◽  
Tian Xiao ◽  
Ying Wu ◽  
Feng Zhou ◽  
Wuchang Zhang
Keyword(s):  
East China Sea ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Archaeal Community ◽  
Changjiang Estuary ◽  
East China ◽  
The Changjiang Estuary ◽  
China Sea ◽  
Gradient Gel Electrophoresis ◽  
Archaeal Communities

The archaeal community and the effects of environmental factors on microbial community distribution were investigated at five sampling sites in the Changjiang Estuary hypoxia area and the adjacent East China Sea in June, August, and October 2006. Profiles of the archaeal communities were generated by denaturing gradient gel electrophoresis of 16S rRNA genes followed by DNA sequence analysis, and the results were analyzed by multivariate statistical analysis. Denaturing gradient gel electrophoresis band patterns were analyzed by cluster analysis to assess temporal changes in the genetic diversity of the archaeal communities. Most of the October samples grouped together separately from those of June and August. Analysis of DNA sequences revealed that the dominant archaeal groups in the Changjiang Estuary hypoxia area and the adjacent East China Sea were affiliated with Euryarchaeota (mainly marine group II) and Crenarchaeota. The effects of environmental factors on the archaeal community distribution were analyzed by the ordination technique of canonical correspondence analysis. Salinity had a significant effect on the archaeal community composition.

Novel soil lineages ofArchaeaare present in semi-arid soils of eastern Australia

2007 ◽  
Vol 53 (1) ◽  
pp. 129-138 ◽  
Author(s):  
David J Midgley ◽  
Jennifer A Saleeba ◽  
Michael I Stewart ◽  
Peter A McGee
Keyword(s):  
Restriction Analysis ◽  
Archaeal Community ◽  
Rdna Sequencing ◽  
Eastern Australia ◽  
Dna Restriction ◽  
Semi Arid Region ◽  
Agricultural Site ◽  
Derived Data ◽  
Archaeal Communities ◽  
Semi Arid

The diversity of Archaea was studied in vertisolic and loam soils of a semi-arid region in Australia. Sampling was undertaken at an agricultural site, two grassland environments, and a brigalow (Acacia harpophylla) woodland. Archaeal community structure was profiled using amplified ribosomal DNA restriction analysis (ARDRA) combined with rDNA sequencing of an example of each restriction fragment length polymorphism type. Sequence comparison and phylogenetic analysis demonstrated that both crenarchaeotal and euryarchaeotal Archaea were present at oxic depths in the soil at all field sites. Along with previously described soil archaeal lineages, novel soil lineages and the deeply divergent Pendant-33 group of Euryarchaeota were also detected. A novel statistical method for comparing ARDRA derived data was demonstrated and implemented using the archaeal communities from the four field sites. Archaeal diversity, as measured by this method, was significantly higher in the agricultural site than at either of the grassland sites or the brigalow woodland.Key words: archaeal communities, cotton, Euryarchaeota, Crenarchaeota, soil.

scholarly journals Distribution of Archaea in a Black Smoker Chimney Structure

2001 ◽  
Vol 67 (8) ◽  
pp. 3618-3629 ◽  
Author(s):  
Ken Takai ◽  
Tetsushi Komatsu ◽  
Fumio Inagaki ◽  
Koki Horikoshi
Keyword(s):  
Enrichment Culture ◽  
Archaeal Community ◽  
Polymorphism Analysis ◽  
Community Structures ◽  
Black Smoker ◽  
Culture Methods ◽  
X Ray ◽  
Combined Use ◽  
Culture Independent ◽  
Archaeal Communities

ABSTRACT Archaeal community structures in microhabitats in a deep-sea hydrothermal vent chimney structure were evaluated through the combined use of culture-independent molecular analyses and enrichment culture methods. A black smoker chimney was obtained from the PACMANUS site in the Manus Basin near Papua New Guinea, and subsamples were obtained from vertical and horizontal sections. The elemental composition of the chimney was analyzed in different subsamples by scanning electron microscopy and energy-dispersive X-ray spectroscopy, indicating that zinc and sulfur were major components while an increased amount of elemental oxygen in exterior materials represented the presence of oxidized materials on the outer surface of the chimney. Terminal restriction fragment length polymorphism analysis revealed that a shift in archaeal ribotype structure occurred in the chimney structure. Through sequencing of ribosomal DNA (rDNA) clones from archaeal rDNA clone libraries, it was demonstrated that the archaeal communities in the chimney structure consisted for the most part of hyperthermophilic members and extreme halophiles and that the distribution of such extremophiles in different microhabitats of the chimney varied. The results of the culture-dependent analysis supported in part the view that changes in archaeal community structures in these microhabitats are associated with the geochemical and physical dynamics in the black smoker chimney.

Sign in / Sign up

Export Citation Format

Share Document