Seasonal Dynamics of Bathyarchaeota-Dominated Benthic Archaeal Communities Associated with Seagrass (Zostera japonica) Meadows

Little is known about the seasonal dynamic of archaeal communities and their potential ecological functions in temperate seagrass ecosystems. In this study, seasonal changes in diversity, community structure, and potential metabolic functions of benthic archaea in surface sediments of two seagrass meadows along the northern Bohai Sea in China were investigated using Miseq sequencing of the 16S rRNA gene and Tax4Fun2 functional prediction. Overall, Crenarchaeota (mainly Bathy-15, Bathy-8, and Bathy-6) dominated, followed by Thermoplasmatota, Asgardarchaeota, and Halobacterota, in terms of alpha diversities and relative abundance. Significant seasonal changes in the entire archaeal community structure were observed. The major phyla Methanobacteria, Nitrosopumilales, and genus Methanolobus had higher proportions in spring, while MBG-D and Bathyarchaeota were more abundant in summer and autumn, respectively. Alpha diversities (Shannon and Simpson) were the highest in summer and the lowest in autumn (ANOVA test, p < 0.05). Salinity, total organic carbon, and total organic nitrogen were the most significant factors influencing the entire archaeal community. Higher cellulose and hemicellulose degradation potentials occurred in summer, while methane metabolism potentials were higher in winter. This study indicated that season had strong effects in modulating bsenthic archaeal diversity and functional potentials in the temperate seagrass ecosystems.

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Spatial-temporal dynamics and influencing factors of archaeal communities in the sediments of Lancang River cascade reservoirs (LRCR), China

PLoS ONE ◽

10.1371/journal.pone.0253233 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0253233

Author(s):

Bo Yuan ◽

Wei Wu ◽

Mengjing Guo ◽

Xiaode Zhou ◽

Shuguang Xie

Keyword(s):

Community Structure ◽

16S Rrna ◽

Large Scale ◽

Temporal Dynamics ◽

Archaeal Community ◽

Rrna Gene ◽

Regulated Rivers ◽

Cascade Reservoirs ◽

Lancang River ◽

Archaeal Communities

The spatial and temporal distribution of the archaeal community and its driving factors in the sediments of large-scale regulated rivers, especially in rivers with cascade hydropower development rivers, remain poorly understood. Quantitative PCR (qPCR) and Illumina MiSeq sequencing of the 16S rRNA archaeal gene were used to comprehensively investigate the spatiotemporal diversity and structure of archaeal community in the sediments of the Lancang River cascade reservoirs (LRCR). The archaeal abundance ranged from 5.11×104 to 1.03×106 16S rRNA gene copies per gram dry sediment and presented no temporal variation. The richness, diversity, and community structure of the archaeal community illustrated a drastic spatial change. Thaumarchaeota and Euryyarchaeota were the dominant archaeal phyla in the sediments of the cascade rivers, and Bathyarchaeota was also an advantage in the sediments. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and carbon and nitrogen metabolism in downstream reservoirs, indicating that anthropogenic pollution discharges might act as the dominant selective force to alter the archaeal communities. Nitrate and C/N ratio were found to play important roles in the formation of the archaeal community composition. In addition, the sediment archaeal community structure was also closely related to the age of the cascade reservoir and hydraulic retention time (HRT). This finding indicates that the engineering factors of the reservoir might be the greatest contributor to the archaeal community structure in the LRCR.

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Axial Differences in Community Structure ofCrenarchaeota and Euryarchaeota in the Highly Compartmentalized Gut of the Soil-Feeding TermiteCubitermes orthognathus

Applied and Environmental Microbiology ◽

10.1128/aem.67.10.4880-4890.2001 ◽

2001 ◽

Vol 67 (10) ◽

pp. 4880-4890 ◽

Cited By ~ 88

Author(s):

Michael W. Friedrich ◽

Dirk Schmitt-Wagner ◽

Tillmann Lueders ◽

Andreas Brune

Keyword(s):

Community Structure ◽

Archaeal Community ◽

Small Subunit ◽

Ssu Rdna ◽

Ecological Niches ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Rdna Sequences ◽

Electron Sink ◽

Archaeal Communities

ABSTRACT Methanogenesis represents an important electron sink reaction in the hindgut of soil-feeding termites. This is the first comprehensive analysis of the archaeal community structure within the highly compartmentalized intestinal tract of a humivorous insect, combining clonal analysis and terminal restriction fragment (T-RF) length polymorphism (T-RFLP) fingerprinting of the archaeal communities in the different gut compartments of Cubitermes orthognathus. We found that the morphological and physicochemical heterogeneity of the gut is reflected in a large phylogenetic diversity and pronounced axial differences in the composition of the archaeal gut microbiota, notably among those clones or ribotypes that could be assigned to methanogenic taxa. Comparative analysis of the relative frequencies of different archaeal lineages among the small-subunit rRNA gene (SSU rDNA) clones and their corresponding T-RF indicated that the archaeal community in the anterior, extremely alkaline hindgut compartment (P1) consists mainly of members of theMethanosarcinaceae, whereasMethanobacteriaceae andMethanomicrobiales predominate in the subsequent, more posterior compartments (P3/4a and P4b). The relative abundance ofThermoplasmales increased towards the rectum (P5). SSU rDNA sequences representing Crenarchaeota, which have not yet been reported to occur in the intestinal tracts of arthropods, were detected in all gut sections. We discuss how the spatial distribution of methanogenic populations may be linked to axial heterogeneity in the physicochemical gut conditions and to functional adaptations to their respective ecological niches.

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Phylogenetic Diversity of Archaea and the Archaeal Ammonia Monooxygenase Gene in Uranium Mining-Impacted Locations in Bulgaria

Archaea ◽

10.1155/2014/196140 ◽

2014 ◽

Vol 2014 ◽

pp. 1-10 ◽

Cited By ~ 4

Author(s):

Galina Radeva ◽

Anelia Kenarova ◽

Velina Bachvarova ◽

Katrin Flemming ◽

Ivan Popov ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Archaeal Community ◽

Uranium Mining ◽

Uranium Mine ◽

Rrna Gene ◽

Ammonia Monooxygenase ◽

Gene Sequences ◽

Monooxygenase Gene ◽

Archaeal Communities

Uranium mining and milling activities adversely affect the microbial populations of impacted sites. The negative effects of uranium on soil bacteria and fungi are well studied, but little is known about the effects of radionuclides and heavy metals on archaea. The composition and diversity of archaeal communities inhabiting the waste pile of the Sliven uranium mine and the soil of the Buhovo uranium mine were investigated using 16S rRNA gene retrieval. A total of 355 archaeal clones were selected, and their 16S rDNA inserts were analysed by restriction fragment length polymorphism (RFLP) discriminating 14 different RFLP types. All evaluated archaeal 16S rRNA gene sequences belong to the 1.1b/Nitrososphaeracluster of Crenarchaeota. The composition of the archaeal community is distinct for each site of interest and dependent on environmental characteristics, including pollution levels. Since the members of 1.1b/Nitrososphaeracluster have been implicated in the nitrogen cycle, the archaeal communities from these sites were probed for the presence of the ammonia monooxygenase gene (amoA). Our data indicate thatamoA gene sequences are distributed in a similar manner as in Crenarchaeota, suggesting that archaeal nitrification processes in uranium mining-impacted locations are under the control of the same key factors controlling archaeal diversity.

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

10.21203/rs.3.rs-34088/v2 ◽

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.

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Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey

Applied and Environmental Microbiology ◽

10.1128/aem.03430-16 ◽

2017 ◽

Vol 83 (12) ◽

Cited By ~ 12

Author(s):

Anna Neubeck ◽

Li Sun ◽

Bettina Müller ◽

Magnus Ivarsson ◽

Hakan Hosgörmez ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Archaeal Community ◽

Resistant Bacteria ◽

Rrna Gene ◽

Content Type ◽

Metal Levels ◽

Gas Seepage ◽

Points Of View

ABSTRACT The surface waters at the ultramafic ophiolitic outcrop in Chimaera, Turkey, are characterized by high pH values and high metal levels due to the percolation of fluids through areas of active serpentinization. We describe the influence of the liquid chemistry, mineralogy, and H2 and CH4 levels on the bacterial community structure in a semidry, exposed, ultramafic environment. The bacterial and archaeal community structures were monitored using Illumina sequencing targeting the 16S rRNA gene. At all sampling points, four phyla, Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria, accounted for the majority of taxa. Members of the Chloroflexi phylum dominated low-diversity sites, whereas Proteobacteria dominated high-diversity sites. Methane, nitrogen, iron, and hydrogen oxidizers were detected as well as archaea and metal-resistant bacteria. IMPORTANCE Our study is a comprehensive microbial investigation of the Chimaera ophiolite. DNA has been extracted from 16 sites in the area and has been studied from microbial and geochemical points of view. We describe a microbial community structure that is dependent on terrestrial, serpentinization-driven abiotic H2, which is poorly studied due to the rarity of these environments on Earth.

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Comparative Analysis of Bacterial and Archaeal Community Structure in Microwave Pretreated Thermophilic and Mesophilic Anaerobic Digesters Utilizing Mixed Sludge under Organic Overloading

Water ◽

10.3390/w12030887 ◽

2020 ◽

Vol 12 (3) ◽

pp. 887 ◽

Cited By ~ 4

Author(s):

Gokce Kor-Bicakci ◽

Emine Ubay-Cokgor ◽

Cigdem Eskicioglu

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

High Throughput Sequencing ◽

Biogas Production ◽

Archaeal Community ◽

Rrna Gene ◽

Anaerobic Digesters ◽

Pretreatment Conditions ◽

The Impact

The effects of microwave (MW) pretreatment were investigated by six anaerobic digesters operated under thermophilic and mesophilic conditions at high organic loading rates (4.9–5.7 g volatile solids/L/d). The experiments and analyses were mainly designed to reveal the impact of MW pretreatment and digester temperatures on the process stability and microbial community structure by correlating the composition of microbial populations with volatile fatty acid (VFA) concentrations. A slight shift from biogas production (with a reasonable methane content) to VFA accumulation was observed in the thermophilic digesters, especially in the MW-irradiated reactors. Microbial population structure was assessed using a high-throughput sequencing of 16S rRNA gene on the MiSeq platform. Microbial community structure was slightly affected by different MW pretreatment conditions, while substantially affected by the digester temperature. The phylum Bacteroidetes proliferated in the MW-irradiated mesophilic digesters by resisting high-temperature MW (at 160 °C). Hydrogenotrophic methanogenesis (mostly the genus of Methanothermobacter) was found to be a key route of methane production in the thermophilic digesters, whereas aceticlastic methanogenesis (mostly the genus of Methanosaeta) was the main pathway in the mesophilic digesters.

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Planktonic Bacterial and Archaeal Communities in an Artificially Irrigated Estuarine Wetland: Diversity, Distribution, and Responses to Environmental Parameters

Microorganisms ◽

10.3390/microorganisms8020198 ◽

2020 ◽

Vol 8 (2) ◽

pp. 198

Author(s):

Mingyue Li ◽

Tiezhu Mi ◽

Zhigang Yu ◽

Manman Ma ◽

Yu Zhen

Keyword(s):

16S Rrna ◽

Microbial Communities ◽

High Throughput Sequencing ◽

Environmental Parameters ◽

Archaeal Community ◽

Rrna Gene ◽

Liaohe River ◽

Estuarine Wetland ◽

Bacterial And Archaeal Communities ◽

Archaeal Communities

Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO4-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities.

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Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites

Archaea ◽

10.1155/2019/5108012 ◽

2019 ◽

Vol 2019 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Pengfei Zheng ◽

Chuantao Wang ◽

Xiaoli Zhang ◽

Jun Gong

Keyword(s):

Community Structure ◽

Zostera Marina ◽

High Throughput Sequencing ◽

Archaeal Community ◽

Distribution Patterns ◽

16S Rrna Genes ◽

Rrna Genes ◽

Absolute Abundance ◽

Bare Sediment ◽

Archaeal Communities

Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, Woesearchaeota and Bathyarchaeota were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (P<0.05), while Thaumarchaeota was favored in unvegetated sites (P=0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community, Bathyarchaeota, and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments (P<0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of Woesearchaeota and Bathyarchaeota, in terms of both relative proportions and absolute quantities.

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Effects of organic loading rate on reactor performance and archaeal community structure in mesophilic anaerobic digesters treating municipal sewage sludge

Waste Management & Research ◽

10.1177/0734242x11417985 ◽

2011 ◽

Vol 29 (11) ◽

pp. 1117-1123 ◽

Cited By ~ 12

Author(s):

Eddie Gómez ◽

Jay Martin ◽

Frederick C. Michel

Keyword(s):

Organic Matter ◽

Community Structure ◽

Community Dynamics ◽

Loading Rate ◽

Archaeal Community ◽

Full Scale ◽

Municipal Sewage Sludge ◽

Organic Loading Rate ◽

Rrna Gene ◽

Organic Loading

In this study, the organic loading rate (OLR) of a high-solids anaerobic digestion (HSAD) system was increased from 3.4 to 5.0 gVS L−1 day−1 and reactor stability, performance and microbial community structure were determined. Laboratory simulations (3.5 L) of the full-scale process (500 dry ton year−1) were conducted using continuously stirred-tank mesophilic reactors. OLRs of 3.4 gVS L−1day−1 (equal to the full-scale HSAD), 4.0, 4.5 and 5.0 gVS L−1day−1 were evaluated. Biochemical parameters and archaeal community dynamics were measured over 42 days of steady state operation. Results showed that increasing OLR increased the amount of organic matter conversion and resulted in higher organic matter removal and volumetric methane (CH4) production (VMP) rates. The highest volatile solids (VS) removal and VMP results of 54 ± 2% and 1.4 ± 0.1 L CH4 L−1day−1 were observed for 5.0 gVS L−1 day−1. The efficiency of reactor conversion of organic matter to CH4 was found to be similar in all the treatments with an average value of 0.57 ± 0.07 LCH4 gVS−1removed. 16S rRNA gene terminal restriction fragment polymorphism (T-RFLP) analyses revealed that archaeal TRFs remained stable during the experiment accounting for an average relative abundance (RA) of 81 ± 1%. Archaea consistent with multiple terminal restriction fragments (TRFs) included members of the Euryarchaeota and Crenarchaeota phyla, including acetoclastic and hydrogenotrophic groups. In conclusion, this laboratory-scale study suggests that performance and stability as well as the archaeal community structure in this HSAD system was unaffected by increasing the OLR by nearly 50% and that this increase resulted in a similar increase in the amount of CH4 gas generated.

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Community structure, distribution pattern, and influencing factors of soil Archaea in the construction area of a large-scale photovoltaic power station

10.21203/rs.3.rs-810369/v1 ◽

2021 ◽

Author(s):

Wei Wu ◽

bo yuan ◽

Shengjuan Yue ◽

Penghui Zou ◽

Ruoting Yang ◽

...

Keyword(s):

Community Structure ◽

Environmental Factors ◽

Distribution Pattern ◽

Archaeal Community ◽

Community Diversity ◽

Power Station ◽

Photovoltaic Power ◽

Significant Difference ◽

Bare Land ◽

Archaeal Communities

Abstract The photovoltaic power station in Qinghai has been built for 8 years, however, its impact on the regional soil ecological environment has not been studied in depth. To reveal the structure and distribution pattern of archaeal communities in desert soil under the influence of a large photovoltaic power station, a comparative study was carried out between the soil affected by photovoltaic panels and the bare land samples outside the photovoltaic station in Gonghe, Qinghai Province. The abundance, community structure, diversity, and distribution characteristics of archaea were analyzed by quantitative PCR and Illumina-MiSeq high-throughput sequencing, and the main environmental factors affecting the variation of soil archaeal community were identified by RDA. The contribution rate of environmental factors and human factors to microbial community diversity was quantitatively evaluated by VPA. The results showed that there was no significant difference in soil nutrients and other physicochemical factors between the photovoltaic power station and bare land. Thaumarchaeota was the dominant archaeal phylum in the area, accounting for more than 99% of archaeal phylum, while at the level of genus, Nitrososphaera was the dominant archaeal genera. There was no significant difference in archaeal community structure between and under different types of PV panels. The analysis has shown that the construction of a photovoltaic station has little effect on the community structure of soil archaea in a desert area, and it was speculated that the selection of niche played a leading role in the distribution pattern of soil archaeal community. This study provides the basis for a scientific understanding of the characteristics and distribution patterns of soil archaeal communities affected by the construction of a photovoltaic power station.

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