Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota

Xie, Yuan-Guo; Luo, Zhen-Hao; Fang, Bao‐Zhu; Jiao, Jian‐Yu; Xie, Qijun; Cao, Xing-Ru; Qu, Yan-Ni; Qi, Yan-Lin; Rao, Yang-Zhi; Li, Yuxian; Liu, Yonghong; Li, Andrew; Seymour, Cale O.; Palmer, Marike; Hedlund, Brian P.; Li, Wenjun; Hua, Zheng-Shuang

doi:10.1186/s40168-022-01376-y

Cited by 16 publications

(11 citation statements)

References 77 publications

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“…[15,[78][79][80][81][82][83]. Within putatively novel phyla, a higher diversity of Patescibacteria and Nanoarchaeota has been observed in hypersaline lake environments compared to other environments, aligning with previous findings of saline lake studies [15,24]. Some MAGs, such as Caldatribacteriota and KSB1, were rarely reported in other environments except marine sediments [84,85] or, as is the case of Margulisbacteria in underground water environments [86].…”

Section: Discussionsupporting

confidence: 83%

“…3d). These archaea have been considered as symbionts, exhibiting intracellular lifestyles with other prokaryotic cells [24, 64]. Several putatively novel phyla were exclusively identified in ADH and BLK sediments (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Consequently, many microbial communities in these hypersaline habitats remain unexplored, presenting potential resources for biotechnological applications [19][20][21][22]. Genomeresolved analyses indicates that these deep inland hypersaline lakes many uncultured microorganisms, namely microbial dark matters (MDMs), such as DPANN archaea and CPR bacteria [15,23,24]. These findings substantially broadened our recognition of MDMs from an evolutionary perspective.…”

Section: Introductionmentioning

confidence: 99%

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Unravelling Biosynthesis and Biodegradation Potentials of Microbial Dark Matters in Hypersaline Lakes

Qiu

Zhu

Zhang

et al. 2023

Preprint

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Biosynthesis and biodegradation of microorganisms critically underpin the development of biotechnology, new drugs and therapies, and environmental remediation. However, the vast majority of uncultured microbial species along with their metabolic capacities in extreme environments remain obscured. To unravel the metabolic potential of these microbial dark matters (MDMs), we investigated four deep-inland hypersaline lakes with largely diversified environmental parameters in Xinjiang, China. Metagenomic binning obtained 3,030 metagenome-assembled genomes (MAGs) spanning 82 phyla, of which 2,363 MAGs could not be assigned to a known genus. MDM MAGs were abundantly observed with distinct taxa among lakes, possibly linked to the diversification of physiochemical conditions. Analysis of biosynthetic potentials identified 9,635 biosynthesis gene clusters (BGCs), in which 8,966 BGCs considered novel. We found that some MDM phyla consistently comprised enriched BGCs, which were considered to play essential roles in biotechnological applications. In addition, biodegradation potentials such as dehalogenation, anaerobic ammonium oxidation (Anammox), polycyclic aromatic hydrocarbon (PAH), and plastics degradation were found in new microbial clades from hypersaline lakes. These findings substantially expanded the genetic repository of biosynthesis and biodegradation potentials, which can further assist the development of new and innovative applications in biotechnology.

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Section: Discussionsupporting

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Unravelling Biosynthesis and Biodegradation Potentials of Microbial Dark Matters in Hypersaline Lakes

Qiu

Zhu

Zhang

et al. 2023

Preprint

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“…Interestingly, two of the received MAGs belong to the Nanosalinaceae family which is a part of the phylum Nanohaloarchaeota, which is part of DPANN superphylum. This taxon includes non-cultured microorganisms living in symbiosis with Halobacteria, characterized by small genomes and limited metabolic capabilities (Castelle et al 2018 ; Xie et al 2022 ). Due to the still incomplete characterization of microorganisms belonging to the Nanohaloarchaeota, the obtained MAGs may bring significant value to further research.…”

Section: Discussionmentioning

confidence: 99%

A first insight into the Polish Bochnia Salt Mine metagenome

Lach

Królikowska

Baranowska

et al. 2023

Environ Sci Pollut Res

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The Bochnia Salt Mine is one of the oldest mines in Europe. It was established in the thirteenth century, and actively operated until 1990. The mine has been placed on the UNESCO World Heritage List. Previous research describing Polish salt mines has been focused on bioaerosol characteristics and the identification of microorganisms potentially important for human health. The use of Polish salt mines as inhalation chambers for patients of health resorts has also been investigated. Nevertheless, the biodiversity of salt mines associated with biotechnological potential has not been well characterized. The present study paper examines the biodiversity of microorganisms in the Bochnia Salt Mine based on 16S rRNA gene and shotgun sequencing. Biodiversity studies revealed a significantly higher relative abundance of Chlamydiae at the first level of the mine (3.5%) compared to the other levels (< 0.1%). Patescibacteria microorganisms constituted a high percentage (21.6%) in the sample from site RA6. Shotgun sequencing identified 16 unique metagenome-assembled genomes (MAGs). Although one was identified as Halobacterium bonnevillei, the others have not yet been assigned to any species; it is possible that these species may be undescribed. Preliminary analyses of the biotechnological and pharmaceutical potential of microorganisms inhabiting the mine were also performed, and the biosynthetic gene cluster (BGC) profiles and antimicrobial peptide (AMP) coding genes in individual samples were characterized. Hundreds of BGCs and dozens of AMP coding genes were identified in metagenomes. Our findings indicate that Polish salt mines are promising sites for further research aimed at identifying microorganisms that are producers of potentially important substances with biotechnological and pharmaceutical applications.

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“…Both the binned genomes showed that they have genes associated with DNA replication, DNA repair, transcription, and translation but lack the biosynthetic capacity to synthesize nucleotides, a few amino acids, lipids, and other cofactors. The absence of such essential biosynthetic pathways implies that they may likely have a symbiotic lifestyle (Xie et al, 2022). The binned genomes also showed the presence of partial tricarboxylic acid (TCA) cycle and capability of the archaea in having anaerobic metabolism.…”

Section: Discussionmentioning

confidence: 99%

Characterization of metagenome-assembled genomes of two endo-archaea of Candida tropicalis

Jagadeeshwari¹,

Sasikala²,

Rai³

et al. 2023

Front. Microbiomes

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IntroductionHost-microbe interactions are pivotal in host biology, ecology, and evolution. Recent developments in sequencing technologies have provided newer insights into the same through the hologenome concept.MethodsWe report here the study on metagenome-assembled genomes (MAGs) associated with Candida tropicalis (studied through shotgun metagenome sequencing), adding to the knowledge about endomicrobiomes of yeast. De novo assembly and binning recovered two partial archaeal genomes, taxonomically belonging to the phylum Asgardarchaeota.Results and DiscussionThe phylogenomic analysis based on the core genes revealed that both the binned genomes cladded separately with the less studied and uncultivated ‘Candidatus’ superphylum, designated as Asgard archaea (the nearest known relative of eukaryotes). Between the two binned genomes, the average nucleotide index (ANI) was 71.2%. The average nucleotide identities (ANI) of the two binned genomes with ‘Candidatus Heimdallarchaeota’ were 60.4-61.2%. The metabolic pathways of both the binned genomes predicted genes belonging to sulfur reduction, Kreb’s pathway, glycolysis, and C1 carbon metabolism. Further, both the binned genomes were predicted to support autotrophic as well as the heterotrophic mode of growth, which might probably help the host in its nutritional requirements also. Further, the genomes showed few eukaryotic signature proteins (ESPs) and SNARE proteins indicating that members of Asgardarchaeota are the closest relatives of eukaryotes. The gaps present in the metabolic potential of the MAGs obtained and the absence of a few essential pathways shows that they are probably in a symbiotic relationship with the host. The present study, reports for the first-time endosymbiosis of Asgard archaea with yeast. It also provides insights into the metabolic potential, ecology, evolutionary history, and endosymbiotic nature of the important but 160 poorly studied Asgard archaea.

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Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota

Cited by 16 publications

References 77 publications

Unravelling Biosynthesis and Biodegradation Potentials of Microbial Dark Matters in Hypersaline Lakes

Unravelling Biosynthesis and Biodegradation Potentials of Microbial Dark Matters in Hypersaline Lakes

A first insight into the Polish Bochnia Salt Mine metagenome

Characterization of metagenome-assembled genomes of two endo-archaea of Candida tropicalis

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