Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota

Huang, Wen-Cong; Liu, Yang; Zhang, Xinxu; Zhang, Cui-Jing; Zou, Dayu; Zheng, Shiling; Xü, Wei; Luo, Zengwei; Liu, Fanghua; Li, Meng

doi:10.1038/s41467-021-25565-9

Cited by 34 publications

(25 citation statements)

References 105 publications

(199 reference statements)

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“…Their survival depends on organic matter in the environment and their abundance and diversity are closely related to the abundance of organic matter ( Liu et al, 2018 ). They are more common in salt marsh environments ( Huang et al, 2021 ), suggesting that they may be more likely to survive and thrive in a high salinity environment. In other words, the saltier unconfined groundwater at the G1 and G2 monitoring sites provides a more suitable environment for Woesearchaeales.…”

Section: Discussionmentioning

confidence: 99%

Microbial Diversity in Groundwater and Its Response to Seawater Intrusion in Beihai City, Southern China

Long²,

Sun

et al. 2022

Front. Microbiol.

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Seawater intrusion is a major concern commonly found in coastal aquifers worldwide. Because of the intense aquifer exploitation and land-based marine aquaculture in the coastal area of Beihai City, Guangxi Zhuang Autonomous Region, China, numerous underground aquifers in this area have been affected by seawater intrusion. However, the microbial communities in freshwater aquifers and their response to seawater intrusion are still unclear. In this study, groundwater from three aquifers was collected from three monitoring sites at different distances from the coastline in the coastal area of Beihai City, and the hydrochemical characteristics of these groundwater samples and the structure of the associated microbial communities were analyzed. The Cl− concentration of the samples indicated that seawater intrusion had occurred in the research area up to 1.5 km away from the coastline, but the monitoring site 2 km away from the coastline had yet to be affected. Statistical analysis showed that the bacterial communities in different groundwater aquifers were significantly correlated with the Cl− concentration, thereby suggesting that the extent of seawater intrusion might be one of the primary factors shaping bacterial composition in groundwater of this area, but the composition and distribution of archaea did not show a significant response to seawater intrusion and presented no apparent correlation with the Cl− concentration. α-, γ-Proteobacteria and Bacteroidota were the dominant bacterial lineages, accounting for about 58–95% of the bacterial communities. Meanwhile, the predominant archaeal taxa were mainly composed of Crenarchaeota, Nanoarchaeota, and Thermoplasmatota, as accounting for 83–100%. Moreover, there was significant spatial heterogeneity of microbial communities in the aquifers affected by varying degrees of seawater intrusion. The microbial communities inhabiting the unconfined aquifer were influenced by the geochemical fluctuation caused by seawater infiltration from land-based marine aquaculture ponds and the diffusion of eutrophic surface water. In contrast, changes in microbial community structure in the confined aquifers were closely related to the environmental gradient caused by different degrees of seawater intrusion. In addition, we also found that the tidal cycle did not significantly affect the structure of microbial communities inhabiting confined aquifers that had been long affected by seawater intrusion.

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Section: Discussionmentioning

confidence: 99%

Microbial Diversity in Groundwater and Its Response to Seawater Intrusion in Beihai City, Southern China

Long²,

Sun

et al. 2022

Front. Microbiol.

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“…The comparative genomic analysis was performed by referring to the published research (41, 42, 69). Briefly, orthogroups were found from the genome set (20 “ Ca .…”

Section: Methodsmentioning

confidence: 99%

“…We retained those orthogroups with 4 or more genes according to the previous literature (69). The genes of identical orthogroup were aligned using MAFFT v7.407 with L-INS-i method of high accuracy (71).…”

Section: Methodsmentioning

confidence: 99%

“…Non-metric Multidimensional Scaling (NMDS) analysis was performed using the metaMDS function with default options in R package vegan v2.5-7 (https://github.com/vegandevs/vegan/). We retained those orthogroups with 4 or more genes according to the previous literature (69). The genes of identical orthogroup were aligned using MAFFT v7.407 with L-INS-i method of high accuracy (71).…”

Section: Comparative Genomic Analysis For Ancestral Reconstructionmentioning

confidence: 99%

“…The root of this species tree was reset using the midpoint method, a built-in function in iTOL (65). To obtain the UFBOOT trees of 1,629 orthogroups, we used IQ-TREE with the same settings (-m, LG+G; -bb, 1000; -wbtl) as in the previous research (69). The frequencies of duplications, transfers (gene transfers from the lineage inside the species tree), losses, and originations (gene transfers from the lineages outside the species tree, or true gene originations), as well as copy numbers of 1,629 orthogroups at each node, were inferred using the way of maximum likelihood estimation (ALEml_undated command) in ALE v0.4 (39).…”

Section: Comparative Genomic Analysis For Ancestral Reconstructionmentioning

confidence: 99%

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Comparative genomic insights into the evolution of Halobacteria-associated “Candidatus Nanohaloarchaeota”

Zhao

Zhang

Kumar³

et al. 2022

Preprint

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The phylum “Candidatus Nanohaloarchaeota” is a representative halophilic lineage within DPANN superphylum. They are characterized by their nanosized cells and symbiotic lifestyle with Halobacteria. However, the development of the symbiosis remains unclear for the lack of genomes located at the transition stage. Here, we performed a comparative genomic analysis of “Ca. Nanohaloarchaeota”. We propose a novel family “Candidatus Nanoanaerosalinaceae” represented by five de-replicated metagenome-assembled genomes obtained from hypersaline sediments and the enrichment cultures of soda-saline lakes. Phylogeny analysis reveals that the novel family are placed at the root of the family “Candidatus Nanosalinaceae” including the well-researched taxa. Most members of “Ca. Nanoanaerosalinaceae” contain lower proportion of putative horizontal gene transfers from Halobacteria than “Ca. Nanosalinaceae”, while they maintain moderately acidic proteomes for hypersaline adaptation of “salt-in” strategy, suggesting that “Ca. Nanoanaerosalinaceae” have not established an intimate association with Halobacteria, and may descend from an intermediate stage. Functional prediction discloses that they exhibit divergent potentials in carbohydrate and organic acids metabolism, and environmental responses. Historical events reconstruction illustrates that the involved genes acquired at the putative ancestors possibly drive the evolutionary and symbiotic divergences. Globally, this research on the new family “Ca. Nanoanaerosalinaceae” enriches the taxonomic and functional diversity of “Ca. Nanohaloarchaeota”, and provides insights into the evolutionary process of “Ca. Nanohaloarchaeota” and their Halobacteria-associated symbiosis.ImportanceDPANN superphylum is a group of archaea widely distributing in various habitats. They generally have small cells, and perform a symbiotic lifestyle with other archaea. The archaeal symbiotic interaction is important to understand microbial community. However, the formation and evolution of the symbiosis between the DPANN lineages and other diverse archaea remain unclear. Based on phylogeny, hypersaline adaptation, functional potentials, and historical events of “Ca. Nanohaloarchaeota”, a representative phylum within the DPANN superphylum, we report a novel family descending from an intermediate stage, and we illustrate the evolutionary process of “Ca. Nanohaloarchaeota” and their Halobacteria-associated symbiosis. Furthermore, we find the acquired genes involved in carbohydrate and organic acids metabolism and environmental responses possibly drive the evolutionary and symbiotic divergences. Altogether, this research helps in understanding the evolution of the archaeal symbiosis, and provides a model for the evolution of the other DPANN lineages.

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Nonlocal Acoustic Moiré Hyperbolic Metasurfaces

Han,

Fan,

et al. 2024

Advanced Materials

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The discovery of the topological transition in twisted bilayer (tBL) materials has attracted considerable attention in nano‐optics. In the analogue of acoustics, however, no such topological transition has been found due to the inherent nondirectional scalar property of sound pressure. In this work, by using a theory‐based nonlocal anisotropic design, we transform the in‐plane acoustic pressure into a spatially distributed vector field using twisted multilayer metasurfaces. So‐called “acoustic magic angle”‐related acoustic phenomena occur, such as nonlocal polariton hybridization and the topological Lifshitz transition. The dispersion becomes flat at the acoustic magic angle, enabling polarized excitations to propagate in a single direction. Moreover, the acoustic topological transition (from hyperbolic to elliptic dispersion) is experimentally observed for the first time as the twist angle continuously changes. This unique characteristic facilitates low‐loss tuneable polariton hybridization at the subwavelength scale. We also experimentally demonstrate a twisted trilayer acoustic metasurface, and find more possibilities for manipulating acoustic waves. These discoveries not only enrich the concepts of moiré physics and topological acoustics but also provide a complete framework of theory and methodologies for explaining the phenomena we observed.This article is protected by copyright. All rights reserved

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Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota

Cited by 34 publications

References 105 publications

Microbial Diversity in Groundwater and Its Response to Seawater Intrusion in Beihai City, Southern China

Microbial Diversity in Groundwater and Its Response to Seawater Intrusion in Beihai City, Southern China

Comparative genomic insights into the evolution of Halobacteria-associated “Candidatus Nanohaloarchaeota”

Nonlocal Acoustic Moiré Hyperbolic Metasurfaces

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