Subgroup level differences of physiological activities in marine Lokiarchaeota

Yin, Xiuran; Cai, Mingwei; Liu, Yang; Zhou, Guowei; Richter-Heitmann, Tim; Aromokeye, David A.; Kulkarni, Ajinkya; Nimzyk, Rolf; Cullhed, Henrik; Zhou, Zhichao; Pan, Jie; Yang, Yuchun; Gu, Ji Dong; Elvert, Marcus; Li, Meng; Friedrich, Michael W.

doi:10.1038/s41396-020-00818-5

Cited by 27 publications

(29 citation statements)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These phyla are highly abundant in sediments, but many of their affiliated subgroups are still microbial “dark matter” with respect to the unknown physiological activities, owed to difficulties to cultivate them under laboratory conditions. Only few studies have reported carbon and energy utilization modes for some of these recently discovered archaea [ 4 , 10 – 12 ], but up to date, metagenome analysis is still the predominant way to predict their physiological capabilities. For example, Bathyarchaeota and some Thermoplasmata possess genes encoding fatty acid oxidation and protein degradation [ 13 – 17 ], and many subgroups of Asgard archaea and Bathyarchaeota may be able to utilize a variety of organic carbon sources [ 6 , 18 – 20 ].…”

Section: Introductionmentioning

confidence: 99%

Catabolic protein degradation in marine sediments confined to distinct archaea

et al. 2022

Self Cite

View full text Add to dashboard Cite

Metagenomic analysis has facilitated prediction of a variety of carbon utilization potentials by uncultivated archaea including degradation of protein, which is a wide-spread carbon polymer in marine sediments. However, the activity of detrital catabolic protein degradation is mostly unknown for the vast majority of archaea. Here, we show actively executed protein catabolism in three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeota subgroup 2c) by RNA- and lipid-stable isotope probing in incubations with different marine sediments. However, highly abundant potential protein degraders Thermoprofundales (MBG-D) and Lokiarchaeota subgroup 3 were not incorporating 13C-label from protein during incubations. Nonetheless, we found that the pathway for protein utilization was present in metagenome associated genomes (MAGs) of active and inactive archaea. This finding was supported by screening extracellular peptidases in 180 archaeal MAGs, which appeared to be widespread but not correlated to organisms actively executing this process in our incubations. Thus, our results have important implications: (i) multiple low-abundant archaeal groups are actually catabolic protein degraders; (ii) the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism, and (iii) catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.

show abstract

Section: Introductionmentioning

confidence: 99%

Catabolic protein degradation in marine sediments confined to distinct archaea

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…This provided the first glimpse into the cell biology of Lokiarchaeota. However, Asgard archaea are highly diverse [6] and the exact branching point of eukaryotes within the superphylum is still uncertain [1,7]. Therefore, visualization of Asgard archaeal cells in the environment is essential for a comprehensive understanding of their cellular structure and morphological diversity.…”

Section: Introductionmentioning

confidence: 99%

Spatial separation of ribosomes and DNA in Asgard archaeal cells

et al. 2021

View full text Add to dashboard Cite

The origin of the eukaryotic cell is a major open question in biology. Asgard archaea are the closest known prokaryotic relatives of eukaryotes, and their genomes encode various eukaryotic signature proteins, indicating some elements of cellular complexity prior to the emergence of the first eukaryotic cell. Yet, microscopic evidence to demonstrate the cellular structure of uncultivated Asgard archaea in the environment is thus far lacking. We used primer-free sequencing to retrieve 715 almost full-length Loki- and Heimdallarchaeota 16S rRNA sequences and designed novel oligonucleotide probes to visualize their cells in marine sediments (Aarhus Bay, Denmark) using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Super-resolution microscopy revealed 1–2 µm large, coccoid cells, sometimes occurring as aggregates. Remarkably, the DNA staining was spatially separated from ribosome-originated FISH signals by 50–280 nm. This suggests that the genomic material is condensed and spatially distinct in a particular location and could indicate compartmentalization or membrane invagination in Asgard archaeal cells.

show abstract

“…Furthermore, they have been described to be able to grow on lignin (Yu et al ., 2018 ). Also for Lokiarchaeota, it is assumed that they have the potential to degrade lignin besides other substrates, such as humic acids, lactate, aromatic compounds and proteins (Yin et al ., 2020 ). The presence of mto homologues in those archaea therefore might suggest that they are able to grow on MACs.…”

Section: Discussionmentioning

confidence: 99%

A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus

Welte

Graaf

Martins

et al. 2021

Environmental Microbiology

View full text Add to dashboard Cite

Methoxylated aromatic compounds (MACs) are important components of lignin found in significant amounts in the subsurface. Recently, the methanogenic archaeon Methermicoccus shengliensis was shown to be able to use a variety of MACs during methoxydotrophic growth. After a molecular survey, we found that the hyperthermophilic non-methanogenic archaeon Archaeoglobus fulgidus also encodes genes for a bacterial-like demethoxylation system. In this study, we performed growth and metabolite analysis, and used transcriptomics to investigate the response of A. fulgidus during growth on MACs in comparison to growth on lactate. We observed that A. fulgidus converts MACs to their hydroxylated derivatives with CO 2 as the main product and sulfate as electron acceptor. Furthermore, we could show that MACs improve the growth of A. fulgidus in the presence of organic substrates such as lactate. We also found evidence that other archaea such as Bathyarchaeota, Lokiarchaeota, Verstraetearchaeota, Korarchaeota, Helarchaeota and Nezhaarchaeota encode a demethoxylation system. In summary, we here describe the first non-methanogenic archaeon with the ability to grow on MACs indicating that methoxydotrophic archaea might play a so far underestimated role in the global carbon cycle.

show abstract

Subgroup level differences of physiological activities in marine Lokiarchaeota

Cited by 27 publications

References 77 publications

Catabolic protein degradation in marine sediments confined to distinct archaea

Catabolic protein degradation in marine sediments confined to distinct archaea

Spatial separation of ribosomes and DNA in Asgard archaeal cells

A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus

Contact Info

Product

Resources

About