Presence of two novel cardiolipins in the halophilic archaeal community in the crystallizer brines from the salterns of Margherita di Savoia (Italy) and Eilat (Israel)

Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.

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

Animals ◽

10.3390/ani11072139 ◽

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.

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Effects of long-acting, broad spectra anthelmintic treatments on the rumen microbial community compositions of grazing sheep

Scientific Reports ◽

10.1038/s41598-021-82815-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Christina D. Moon ◽

Luis Carvalho ◽

Michelle R. Kirk ◽

Alan F. McCulloch ◽

Sandra Kittelmann ◽

...

Keyword(s):

Archaeal Community ◽

Fungal Communities ◽

Control Group ◽

Microbiota Composition ◽

Rumen Microbiota ◽

Treatment Groups ◽

Methanobrevibacter Ruminantium ◽

Group 12 ◽

Relative Abundances ◽

Long Acting

AbstractAnthelmintic treatment of adult ewes is widely practiced to remove parasite burdens in the expectation of increased ruminant productivity. However, the broad activity spectra of many anthelmintic compounds raises the possibility of impacts on the rumen microbiota. To investigate this, 300 grazing ewes were allocated to treatment groups that included a 100-day controlled release capsule (CRC) containing albendazole and abamectin, a long-acting moxidectin injection (LAI), and a non-treated control group (CON). Rumen bacterial, archaeal and protozoal communities at day 0 were analysed to identify 36 sheep per treatment with similar starting compositions. Microbiota profiles, including those for the rumen fungi, were then generated for the selected sheep at days 0, 35 and 77. The CRC treatment significantly impacted the archaeal community, and was associated with increased relative abundances of Methanobrevibacter ruminantium, Methanosphaera sp. ISO3-F5, and Methanomassiliicoccaceae Group 12 sp. ISO4-H5 compared to the control group. In contrast, the LAI treatment increased the relative abundances of members of the Veillonellaceae and resulted in minor changes to the bacterial and fungal communities by day 77. Overall, the anthelmintic treatments resulted in few, but highly significant, changes to the rumen microbiota composition.

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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 ◽

10.1155/2019/3717239 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12 ◽

Cited By ~ 3

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.

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Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes

Applied Microbiology and Biotechnology ◽

10.1007/s00253-016-7318-x ◽

2016 ◽

Vol 100 (10) ◽

pp. 4685-4698 ◽

Cited By ~ 15

Author(s):

Anyi Hu ◽

Hongjie Wang ◽

Jiangwei Li ◽

Jing Liu ◽

Nengwang Chen ◽

...

Keyword(s):

Environmental Changes ◽

Archaeal Community ◽

Southeast China

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Comparison of the archaeal community in the fermentative compartment and faeces of the cow and the rabbit

Anaerobe ◽

10.1016/j.anaerobe.2010.04.004 ◽

2010 ◽

Vol 16 (4) ◽

pp. 396-401 ◽

Cited By ~ 18

Author(s):

Rory Julien Michelland ◽

Valérie Monteils ◽

Sylvie Combes ◽

Laurent Cauquil ◽

Thierry Gidenne ◽

...

Keyword(s):

Archaeal Community

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Archaeal ammonia oxidizers respond to soil factors at smaller spatial scales than the overall archaeal community does in a high Arctic polar oasis

Canadian Journal of Microbiology ◽

10.1139/cjm-2015-0669 ◽

2016 ◽

Vol 62 (6) ◽

pp. 485-491 ◽

Cited By ~ 3

Author(s):

Samiran Banerjee ◽

Nabla Kennedy ◽

Alan E. Richardson ◽

Keith N. Egger ◽

Steven D. Siciliano

Keyword(s):

Community Structure ◽

Spatial Scales ◽

Archaeal Community ◽

Diversity Indices ◽

High Arctic ◽

Total Carbon ◽

Spatial Dependency ◽

Edaphic Factors ◽

Total Carbon Content ◽

Arctic Soils

Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2–5 m scale (P < 0.05), whereas AOA communities were dependent at the ∼1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases.

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