Deciphering symbiotic interactions of ‘Candidatus Aenigmarchaeota’ with inferred horizontal gene transfers and co-occurrence networks

Li, Yuxian; Rao, Yang-Zhi; Qi, Yue; Qu, Yan-Ni; Chen, Yating; Jiao, Jian‐Yu; Shu, Wen‐Sheng; Jiang, Hongchen; Hedlund, Brian P.; Hua, Zheng-Shuang; Li, Wen‐Jun

doi:10.21203/rs.3.rs-17151/v1

Cited by 7 publications

(9 citation statements)

References 73 publications

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“…Other microbes obtained as MAGs included members of the uncultured microbial dark matter, such as Patescibacteria and Nanoarchaeota [6,[37][38][39]. In particular, we have stumbled upon various members of Aenigmarchaeota [40] and Woesearchaeales with their usual streamlined genomes and hard to predict metabolic properties.…”

Section: Discussionmentioning

confidence: 99%

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

Cabello‐Yeves

Callieri

Picazo

et al. 2021

Environmental Microbiome

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Background The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salinity and temperature. Despite its well-known hydrology and physicochemical features, this enormous water mass remains poorly studied at the microbial genomics level. Results We have sampled its different water masses and analyzed the microbiome by shotgun and genome-resolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria (Synechococcus but a conspicuously absent Prochlorococcus), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of “dark matter” streamlined genomes of largely unpredictable ecology. Conclusions The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome.

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Section: Discussionmentioning

confidence: 99%

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

Cabello‐Yeves

Callieri

Picazo

et al. 2021

Environmental Microbiome

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“…Among all of the associated microbiota, we must highlight the presence of Nanoarchaeota [34][35][36][37]. In particular, we have stumbled upon various members of Aenigmarchaeota [38] and Woesearchaeales that showed streamlined genomes. Annotation of contigs was assessed using Prodigal [41] for ORF prediction and then BLAST (nr database) using Diamond for functional annotation [42].…”

Section: Discussionmentioning

confidence: 99%

“…Other exotic members of this system included the uncultured microbial dark matter, such as Patescibacteria and Nanoarchaeota [34][35][36][37]. In particular, we have stumbled upon various members of Aenigmarchaeota [38] and Woesearchaeales that showed streamlined genomes. .001283 E, respectively).…”

Section: Discussionmentioning

confidence: 99%

Microbiome of the Black Sea water column analyzed by genome centric metagenomics

Cabello‐Yeves

Callieri

Picazo

et al. 2020

Preprint

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Background: The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former albeit with lower salinity and (mostly) temperature. In spite of its well-known hydrology and physico chemistry, this enormous water mass remains poorly studied at the microbial genomics level. Results: We have sampled its different water masses and analyzed the microbiome by classic and genome-resolved metagenomics generating a large number of metagenome-assembled genomes (MAGs) from them. The oxic zone presents many similarities to the global ocean while the euxinic water mass has similarities to other similar aquatic environments of marine or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environments and includes Cyanobacteria (Synechococcus), photoheterotrophs (largely with marine relatives), facultative/microaerophilic microbes again largely marine, chemolithotrophs (N and S oxidizers) and a large number of anaerobes, mostly sulfate reducers but also a few methanogens and a large number of 'dark matter' streamlined genomes of largely unpredictable ecology. Conclusions: The Black Sea presents a mixture of similarities to other water bodies. The photic zone has many microbes in common with that of the Mediterranean with the relevant exception of the absence of Prochlorococcus. The chemocline already presents very different characteristics with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. Finally the euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy generating metabolism and a small but detectable methanogenesis.We are adding critical information about this unique and important ecosystem and its microbiome.

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“…Nitrosotaleaceae and Nitrososphaeraceae are ammonia oxidizers able to convert ammonia to nitrate (Alves et al, 2018; Zou et al, 2020), while Aenigmarchaeota are thought to be involved in carbon fixation, or rely on host-symbiont interactions for nutrient acquisition. (Castelle et al, 2015; Li et al, 2020). The archaeal community in the harbour surface water samples was more like the river samples, and this appears to be driven by the higher concentrations of NH 4 emanating from the river along with the lacking of mixing with the subjacent water layer (Hitchcock and Mitrovic, 2015; Wymore et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

The importance of environmental parameters and mixing zone in shaping estuarine microbial communities along a freshwater-marine gradient

Silva¹,

White²,

Bowman

et al. 2022

Preprint

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Microbial communities are important elements in the marine environment, contributing to nutrient cycling and biogeochemical processes. Estuaries comprise environments exhibiting characteristics from freshwater to marine, leading to distinct microbial communities across this environmental gradient. Here, we examine the spatial dynamics of microbial communities in Macquarie Harbour, an estuarine system on the West coast of Tasmania, Australia. Water was sampled along the estuary to explore the structure and composition of the microbial communities using 16S/18S rRNA gene amplicon sequencing. Multivariate analyses showed environmental variables and community compositions varying along a longitudinal (river to adjacent ocean) gradient at the surface. In the harbour, differences in the microbial community were observed between surface (0-1 m) and intermediate depths (4.5-11 m depth). The results of differential abundance, network and Partial Least Square analyses suggest that Macquarie Harbour is a mixing zone, where the distributions of archaeal, bacterial and eukaryotic communities are influenced by oceanic and riverine inputs. Coupled with the natural characteristics of the Harbour, the heterotrophic component of this microbial communities inhabiting the surface and intermediate waters may play important roles in the nutrient cycle in the studied area. These results provide critical insights into the Macquarie Harbour environment and the importance of understanding the role of microbial communities for similar systems elsewhere.

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Deciphering symbiotic interactions of ‘Candidatus Aenigmarchaeota’ with inferred horizontal gene transfers and co-occurrence networks

Cited by 7 publications

References 73 publications

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

Microbiome of the Black Sea water column analyzed by genome centric metagenomics

The importance of environmental parameters and mixing zone in shaping estuarine microbial communities along a freshwater-marine gradient

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