New approaches for archaeal genome-guided cultivation

Wang, Yinzhao; Kamagata, Yoichi; Li, Meng; Han, Feifei; Wang, Fengping; Xiao, Xiang

doi:10.1007/s11430-020-9793-5

Cited by 7 publications

(7 citation statements)

References 225 publications

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“…Taxa belonging to prokaryotic families of interest identified here are likely culturable based on the previous culturing success of individual strains within these families [ 59 , 90 – 97 ]. Furthermore, overlaying functional information may help inform genome-guided cultivation for taxa that prove to be more challenging to culture [ 98 ]. In addition, our results show that the involvement of CCA, brown algae and diatoms on A. tenuis larval settlement warrants further investigation.…”

Section: Discussionmentioning

confidence: 99%

Linking differences in microbial network structure with changes in coral larval settlement

Turnlund,

Vanwonterghem,

Botté

et al. 2023

ISME Communications

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Coral cover and recruitment have decreased on reefs worldwide due to climate change-related disturbances. Achieving reliable coral larval settlement under aquaculture conditions is critical for reef restoration programmes; however, this can be challenging due to the lack of reliable and universal larval settlement cues. To investigate the role of microorganisms in coral larval settlement, we undertook a settlement choice experiment with larvae of the coral Acropora tenuis and microbial biofilms grown for different periods on the reef and in aquaria. Biofilm community composition across conditioning types and time was profiled using 16S and 18S rRNA gene sequencing. Co-occurrence networks revealed that strong larval settlement correlated with diverse biofilm communities, with specific nodes in the network facilitating connections between modules comprised of low- vs high-settlement communities. Taxa associated with high-settlement communities were identified as Myxoccales sp., Granulosicoccus sp., Alcanivoraceae sp., unassigned JTB23 sp. (Gammaproteobacteria), and Pseudovibrio denitrificans. Meanwhile, taxa closely related to Reichenbachiella agariperforans, Pleurocapsa sp., Alcanivorax sp., Sneathiella limmimaris, as well as several diatom and brown algae were associated with low settlement. Our results characterise high-settlement biofilm communities and identify transitionary taxa that may develop settlement-inducing biofilms to improve coral larval settlement in aquaculture.

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Section: Discussionmentioning

confidence: 99%

Linking differences in microbial network structure with changes in coral larval settlement

Turnlund,

Vanwonterghem,

Botté

et al. 2023

ISME Communications

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“…However, the Archaea remain largely mysterious as the majority are uncultivated and have no cultured close relatives. Thus, MAGs and SAGs provide access to their genomes and enable inferring key genes for specific functions, metabolism, and phylogenetic relationships 40 , 41 , 42 . Analyses of MAGs have provided strong evidence that members of the Asgard lineage of Archaea may be the closest prokaryotic ancestor to the “nuclear” component of the Eukarya 43 , 44 .…”

Section: The Modern Description Of Prokaryotic Lifementioning

confidence: 99%

Why and how to use the SeqCode

Whitman,

Chuvochina,

Hedlund

et al. 2024

mLife

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The SeqCode, formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data, is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic species. While similar to the International Code of Nomenclature of Prokaryotes (ICNP) in structure and rules of priority, it does not require the deposition of type strains in international culture collections. Thus, it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture collections. Because the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes, the SeqCode is the only code suitable for naming the majority of prokaryotic species. The start date of the SeqCode was January 1, 2022, and the online Registry (https://seqco.de/) was created to ensure valid publication of names. The SeqCode recognizes all names validly published under the ICNP before 2022. After that date, names validly published under the SeqCode compete with ICNP names for priority. As a result, species can have only one name, either from the SeqCode or ICNP, enabling effective communication and the creation of unified taxonomies of uncultured and cultured prokaryotes. The SeqCode is administered by the SeqCode Committee, which is comprised of the SeqCode Community and elected administrative components. Anyone with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.

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“…Marine ecosystems are a vast habitat for diverse metabolically active groups of microbes, including sulfur-oxidizing and polysaccharide-degrading bacteria ( 1 , 2 ). In the context of screening and isolating novel and uncultured metabolically active bacterial strains from marine settings in our laboratory ( 3 – 5 ), four strains have been isolated from sediment samples of the South China Sea (global positioning system [GPS] coordinates, 115.830°E, 18.813°N). The sediment cores were collected using a multicorer, sliced into 2-cm pieces onboard as soon as possible, placed into Nasco sampling bags, and preserved at 4°C.…”

Section: Announcementmentioning

confidence: 99%

Draft Genome Sequences of Four Bacterial Strains Isolated from Sediment of the South China Sea

Ishaq

Ahmad

Hou

et al. 2022

Microbiol Resour Announc

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Here, we report the draft genome sequences of four bacterial isolates from sediment of the South China Sea. Three of the isolates belong to the class Alphaproteobacteria and encode complete SoxXAYZBCD gene clusters, related to thiosulfate oxidation, while one isolate belongs to the class Opitutae and possesses a total of 397 carbohydrate active enzymes (CAZymes), related to predicted polysaccharide degradation.

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New approaches for archaeal genome-guided cultivation

Cited by 7 publications

References 225 publications

Linking differences in microbial network structure with changes in coral larval settlement

Linking differences in microbial network structure with changes in coral larval settlement

Why and how to use the SeqCode

Draft Genome Sequences of Four Bacterial Strains Isolated from Sediment of the South China Sea

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