New globally distributed bacterial phyla within the FCB superphylum DOI Creative Commons
Xianzhe Gong, Álvaro Rodríguez del Río, Xu Le

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Dec. 6, 2022

Abstract Microbes in marine sediments play crucial roles global carbon and nutrient cycling. However, our understanding of microbial diversity physiology on the ocean floor is limited. Here, we use phylogenomic analyses thousands metagenome-assembled genomes (MAGs) from coastal deep-sea to identify 55 MAGs that are phylogenetically distinct previously described bacterial phyla. We propose these belong 4 novel phyla (Blakebacterota, Orphanbacterota, Arandabacterota, Joyebacterota) a proposed phylum (AABM5-125-24), all them within FCB superphylum. Comparison their rRNA genes with public databases reveals globally distributed different habitats, including marine, freshwater, terrestrial environments. Genomic suggest organisms capable mediating key steps sedimentary biogeochemistry, anaerobic degradation polysaccharides proteins, respiration sulfur nitrogen. Interestingly, code for an unusually high proportion (~9% average, up 20% per genome) protein families lacking representatives databases. Genes encoding hundreds colocalize predicted be involved reduction, nitrogen cycling, energy conservation, organic compounds. Our findings advance diversity, ecological bacteria, potential links between gene metabolic processes oceans.

Language: Английский

Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways DOI Creative Commons
Valerie De Anda, Lin-Xing Chen, Nina Dombrowski

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: April 23, 2021

Abstract Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial spring sediments in China deep-sea vent Guaymas Basin, Gulf of California. Phylogenetic analyses these MAGs indicate that they form a distinct group within the TACK superphylum, thus propose their classification new phylum, ‘Brockarchaeota’, named after Thomas Brock his seminal research springs. Based on MAG sequence information, infer some Brockarchaeota uniquely capable mediating non-methanogenic anaerobic methylotrophy, via tetrahydrofolate methyl branch Wood-Ljungdahl pathway reductive glycine pathway. The genotypes appear to be obligate fermenters plant-derived polysaccharides rely mostly substrate-level phosphorylation, seem lack most respiratory complexes. In contrast, lineages have alternate pathways increase ATP yield, including methylotrophy methanol trimethylamine, potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution apparent metabolic versatility may occupy previously overlooked roles cycling.

Language: Английский

Citations

56
Characterization of the first cultured free-living representative of Candidatus Izemoplasma uncovers its unique biology DOI Creative Commons
Rikuan Zheng, Rui Liu,

Yeqi Shan

et al.

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(9), P. 2676 - 2691

Published: March 21, 2021

Abstract Candidatus Izemoplasma, an intermediate in the reductive evolution from Firmicutes to Mollicutes, was proposed represent a novel class of free-living wall-less bacteria within phylum Tenericutes. Unfortunately, paucity pure cultures has limited further insights into their physiological and metabolic features as well ecological roles. Here, we report first successful isolation Izemoplasma representative deep-sea methane seep, strain zrk13, using DNA degradation-driven method given Izemoplasma’s prominent DNA-degradation potentials. We present detailed description physiological, genomic traits strain, which allows for time reconstruction potential lifestyle member tentatively defined Izemoplasma. On basis species genus Xianfuyuplasma coldseepsis is proposed. Using combined biochemical transcriptomic method, show supplement organic matter, thiosulfate or bacterial could evidently promote growth zrk13. In particular, zrk13 degrade utilize extracellular both laboraterial conditions. Moreover, predicted genes determining broadly distribute genomes other members. Given that particularly crucial phosphorus nitrogen carbon source microorganisms seafloor, are thought be important contributors biogeochemical cycling deep ocean.

Language: Английский

Citations

46
Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles DOI Creative Commons
John D Carlton, Marguerite V. Langwig, Xianzhe Gong

et al.

ISME Communications, Journal Year: 2023, Volume and Issue: 3(1)

Published: June 24, 2023

Abstract Marine sediments comprise one of the largest environments on planet, and their microbial inhabitants are significant players in global carbon nutrient cycles. Recent studies using metagenomic techniques have shown complexity these communities identified novel microorganisms from ocean floor. Here, we obtained 77 metagenome-assembled genomes (MAGs) bacterial phylum Armatimonadota Guaymas Basin, Gulf California, Bohai Sea, China. These MAGs two previously undescribed classes within Armatimonadota, which propose naming Hebobacteria Zipacnadia. They globally distributed hypoxic anoxic dominant members deep-sea (up to 1.95% raw reads). The described here also unique metabolic capabilities, possessing pathways reduce dioxide acetate via Wood-Ljungdahl pathway (WLP) generating energy through oxidative branch glycolysis as an electron sink, maintaining redox balance WLP. may be autotrophic, not Armatimonadota. Furthermore, play a role sulfur nitrogen cycling, intermediate compounds hydroxylamine sulfite. Description enhances our understanding diversity potential habitats worldwide.

Language: Английский

Citations

21
Unveiling the impact and mechanisms of Cd-driven ecological assembly and coexistence of bacterial communities in coastal sediments of Yellow Sea DOI

Chengfeng Yu,

Zhiyong Zhu,

Kun Meng

et al.

Journal of Hazardous Materials, Journal Year: 2023, Volume and Issue: 460, P. 132309 - 132309

Published: Aug. 15, 2023

Language: Английский

Citations

18
Adsorption, natural attenuation, and microbial community response of ofloxacin and oxolinic acid in marine sediments DOI

Haiping Li,

Bo Zhang, Fanping Meng

et al.

Environmental Pollution, Journal Year: 2024, Volume and Issue: 347, P. 123738 - 123738

Published: March 6, 2024

Language: Английский

Citations

8
Blue Biotechnology: Marine Bacteria Bioproducts DOI Creative Commons

Karina Maldonado-Ruiz,

R. Pedroza‐Islas,

Lorena Pedraza‐Segura

et al.

Microorganisms, Journal Year: 2024, Volume and Issue: 12(4), P. 697 - 697

Published: March 29, 2024

The ocean is the habitat of a great number organisms with different characteristics. Compared to terrestrial microorganisms, marine microorganisms also represent vast and largely unexplored reservoir bioactive compounds diverse industrial applications like microorganisms. This review examines properties potential products derived from including bacteriocins, enzymes, exopolysaccharides, pigments, juxtaposing them in some cases against their counterparts. We discuss distinct characteristics that set marine-derived apart, enhanced stability unique structural features such as amount uronic acid sulfate groups exopolysaccharides. Further, we explore uses these across various industries, ranging food pharmaceuticals cosmetics biotechnology. presents broad description biotechnologically important produced by bacteria isolated environments, qualities compared

Language: Английский

Citations

7
Spatial dynamics of prokaryotic microbial communities in sediments of the Yellow Sea: Assembly process, co-occurrence relationships, and environmental implications DOI
Huiyuan Qi, Dan Huang,

Fenghe Wang

et al.

Journal of Environmental Management, Journal Year: 2022, Volume and Issue: 319, P. 115645 - 115645

Published: July 4, 2022

Language: Английский

Citations

26
SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis DOI Creative Commons
Jackie Zorz, Carmen Li, Anirban Chakraborty

et al.

ISME Communications, Journal Year: 2023, Volume and Issue: 3(1)

Published: April 20, 2023

Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most work performed far away from sample collection in both space time. Performing amplicon at would have positive implications many instances including remote fieldwork point-of-care medical diagnoses. Here we present SituSeq, an offline portable workflow amplicons using Nanopore standard laptop computer. SituSeq was validated by comparing amplicons, Illumina metagenomes, sequenced same environmental DNA. Comparisons revealed consistent community composition, ecological trends, sequence identity across platforms. Correlation between abundance taxa each taxonomic level data sets high (Pearson's r > 0.9), over 70% sequences matched with greater than 97% identity. On board research vessel on open ocean, used to analyze deep sea sediments less 2 h after sequencing, 8 collection. The rapidly available results informed decisions about subsequent sampling near real-time while offshore expedition still underway. user-friendly helps bring genomics diagnostics more researchers situations.

Language: Английский

Citations

16
Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage ‘Asgard’ archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov. DOI
Hiroyuki Imachi, Masaru K. Nobu, Shingo Kato

et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2024, Volume and Issue: 74(7)

Published: July 5, 2024

An anaerobic, mesophilic, syntrophic, archaeon strain MK-D1

Language: Английский

Citations

6
Globally distributed marine Gemmatimonadota have unique genomic potentials DOI Creative Commons
Xianzhe Gong,

Le Xu,

Marguerite V. Langwig

et al.

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: Aug. 10, 2024

Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles marine environments poorly understood. Here, we obtained 495 metagenome-assembled genomes (MAGs), associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog compare protein composition update phylogeny of these bacteria. The phylogenetically different those previously reported terrestrial environments. Functional analyses revealed genotypes capable degradation complex organic carbon, denitrification, sulfate reduction, oxidizing sulfide sulfite. Interestingly, there is widespread genetic for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source novel natural products. Furthermore, viruses with have "hijack" manipulate host metabolism, including assembly lipopolysaccharide hosts. This diversity advances our understanding globally a variety ecosystems reveals distinctions between communities.

Language: Английский

Citations

6