Two novel species of the family Bacillaceae: Oceanobacillus piezotolerans sp. nov. and Bacillus piezotolerans sp. nov., from deep-sea sediment samples of Yap Trench

Two novel filamentous bacteria, strains SCSIO 11157T and SCSIO 11154T, were isolated from a deep-sea sediment sample. Strain SCSIO 11157T grew optimally at 55–60 °C, while strain SCSIO 11154T grew optimally at 40 °C. Both strains produced aerial and substrate mycelia. Phylogenetic analysis of the 16S rRNA gene sequences of strains SCSIO 11157T and SCSIO 11154T showed that the isolates were affiliated to the family Thermoactinomycetaceae. The two isolates contained ll-diaminopimelic acid as the cell-wall diamino acid, and did not have diagnostic sugars. The major polar lipids of strain SCSIO 11157T were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol, and the major polar lipids of SCSIO 11154T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant menaquinone of both strains was MK-7. The major cellular fatty acids of strain SCSIO 11157T were iso-C15 : 0, C18 : 1ω9c and iso-C17 : 0, and strain SCSIO 11154T contained iso-C15 : 0 and iso-C17 : 0 as major fatty acids. The DNA G+C contents of strains SCSIO 11157T and SCSIO 11154T were 54.2 and 51.8 mol %, respectively. On the basis of its phenotypic and phylogenetic properties, strain SCSIO 11157T represents a novel species in the new genus, for which we propose the name Marinithermofilum abyssi gen. nov., sp. nov. The type strain of Marinithermofilum abyssi is SCSIO 11157T ( = CGMCC 1.15179T = NBRC 109939T). Strain SCSIO 11154T represents a novel species of the genus Desmospora, for which we propose the name Desmospora profundinema sp. nov. The type strain is SCSIO 11154T ( = DSM 45903T = NBRC 109626T).

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The Sulphides of Certain Deep-Sea Sediment Samples Collected on DSDP Leg 31

10.2973/dsdp.proc.31.118.1975 ◽

1975 ◽

Author(s):

K.F.G. Hosking

Keyword(s):

Deep Sea ◽

Deep Sea Sediment ◽

Sediment Samples

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Streptomyces indicus sp. nov., an actinomycete isolated from deep-sea sediment

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.029389-0 ◽

2011 ◽

Vol 61 (11) ◽

pp. 2712-2716 ◽

Cited By ~ 11

Author(s):

Yingxue Luo ◽

Jing Xiao ◽

Yin Wang ◽

Jing Xu ◽

Shujie Xie ◽

...

Keyword(s):

Deep Sea ◽

Novel Species ◽

Diaminopimelic Acid ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Deep Sea Sediment ◽

Diamino Acid ◽

The Indian Ocean ◽

Genotypic Characteristics ◽

Type Strains

The taxonomic position of an actinomycete isolated from deep-sea sediment from the Indian Ocean was determined by using a polyphasic approach. The presence of iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0 as the major cellular fatty acids, ll-diaminopimelic acid as the characteristic diamino acid, and MK-9(H4, H6 and H8) as the major menaquinones supported the affiliation of strain IH32-1T to the genus Streptomyces. Comparison of 16S rRNA gene sequences showed that strain IH32-1T exhibited highest similarities to the type strains of Streptomyces globosus (97.6 %) and Streptomyces toxytricini (97.6 %). However, DNA–DNA relatedness values between strain IH32-1T and the type strains of S. globosus and S. toxytricini were determined as 55.2±4.7 and 38.3±2.5 %, respectively. Based on its chemotaxonomic, phenotypic and genotypic characteristics, strain IH32-1T is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces indicus sp. nov. is proposed. The type strain is IH32-1T ( = DSM 42001T = CGMCC 4.5727T).

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Halomonas zincidurans sp. nov., a heavy-metal-tolerant bacterium isolated from the deep-sea environment

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.051656-0 ◽

2013 ◽

Vol 63 (Pt_11) ◽

pp. 4230-4236 ◽

Cited By ~ 19

Author(s):

Lin Xu ◽

Xue-Wei Xu ◽

Fan-Xu Meng ◽

Ying-Yi Huo ◽

Aharon Oren ◽

...

Keyword(s):

Deep Sea ◽

Copper Ions ◽

Novel Species ◽

Halophilic Bacterium ◽

Rrna Gene ◽

Gram Stain ◽

Content Type ◽

Deep Sea Sediment ◽

Link Type ◽

Moderately Halophilic Bacterium

A Gram-stain-negative, aerobic, rod-like, motile by peritrichous flagella and moderately halophilic bacterium, designated strain B6T, was isolated a deep-sea sediment collected from the South Atlantic Ocean. The isolate grew with 0.5–15 % (w/v) NaCl, at 4–37 °C and pH 5.0–8.5 and showed a high tolerance to zinc, manganese, cobalt and copper ions. The major fatty acids were C16 : 0, C19 : 0 cyclo ω8c, C12 : 0 3-OH and C12 : 0. The predominant ubiquinone was Q-9. The genomic DNA G+C content was 61.1 mol%. Phylogenetic analysis based on 16S rRNA gene comparisons indicated that strain B6T belonged to the genus Halomonas , and the closest relative was Halomonas xinjiangensis TRM 0175T (96.1 %). Based upon the phenotypic, chemotaxonomic and genetic data, strain B6T represents a novel species from the genus Halomonas , for which the name Halomonas zincidurans sp. nov. is proposed. The type strain is B6T ( = CGMCC 1.12450T = JCM 18472T).

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Verrucosispora sediminis sp. nov., a cyclodipeptide-producing actinomycete from deep-sea sediment

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.017053-0 ◽

2010 ◽

Vol 60 (8) ◽

pp. 1807-1812 ◽

Cited By ~ 36

Author(s):

Huan-Qin Dai ◽

Jian Wang ◽

Yu-Hua Xin ◽

Gang Pei ◽

Shu-Kun Tang ◽

...

Keyword(s):

Deep Sea ◽

Phylogenetic Trees ◽

Complete Sequence ◽

Culture Broth ◽

Rrna Gene ◽

The Novel ◽

Deep Sea Sediment ◽

Phenotypic Differences ◽

Distinct Cluster ◽

The Family

An actinomycete, designated MS426T, the culture broth of which showed potent antimicrobial activity, was isolated from a deep-sea sediment sample of the South China Sea. An almost-complete sequence of the 16S rRNA gene of strain MS426T was determined and aligned with those of representatives of the family Micromonosporaceae available in public databases. Phylogenetic trees were inferred by using three algorithms. Strain MS426T formed a branch adjacent to Verrucosispora lutea YIM 013T in a distinct cluster occupied only by strains of the genus Verrucosispora. Strain MS426T was distinguishable from the type strains of the two described Verrucosispora species by using a combination of chemical and morphological markers and by DNA–DNA relatedness. On the basis of these genotypic and phenotypic differences, the novel antimicrobial strain with pharmaceutical potential represents a novel species, for which the name Verrucosispora sediminis sp. nov. is proposed. The type strain is MS426T (=CGMCC 4.3550T =JCM 15670T).

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Shewanella surugensis sp. nov., Shewanella kaireitica sp. nov. and Shewanella abyssi sp. nov., isolated from deep-sea sediments of Suruga Bay, Japan

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64173-0 ◽

2006 ◽

Vol 56 (7) ◽

pp. 1607-1613 ◽

Cited By ~ 41

Author(s):

Masayuki Miyazaki ◽

Yuichi Nogi ◽

Ron Usami ◽

Koki Horikoshi

Keyword(s):

Deep Sea ◽

Type Strain ◽

Gene Sequence ◽

Novel Species ◽

Rrna Gene ◽

Suruga Bay ◽

Deep Sea Sediment ◽

Gene Sequence Analysis ◽

Definition Of ◽

Reference Strains

Six strains representing three novel species were isolated from deep-sea sediment in Suruga Bay, Japan, at a depth of 2406–2409 m. On the basis of 16S rRNA gene sequence analysis, the isolated strains, c931T, c941T, d943, c952, d954 and c959T, are closely affiliated with members of the genus Shewanella. The hybridization values for DNA–DNA relatedness between these strains and Shewanella reference strains were significantly lower than that which is accepted as the phylogenetic definition of a species. On the basis of their distinct taxonomic characteristics, the isolated strains represent three novel Shewanella species, for which the names Shewanella kaireitica sp. nov. (three strains, type strain c931T=JCM 11836T=DSM 17170T), Shewanella abyssi sp. nov. (two strains, type strain c941T=JCM 13041T=DSM 17171T) and Shewanella surugensis sp. nov. (type strain c959T=JCM 11835T=DSM 17177T) are proposed.

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Marseilleviruses: An Update in 2021

Frontiers in Microbiology ◽

10.3389/fmicb.2021.648731 ◽

2021 ◽

Vol 12 ◽

Author(s):

Dehia Sahmi-Bounsiar ◽

Clara Rolland ◽

Sarah Aherfi ◽

Hadjer Boudjemaa ◽

Anthony Levasseur ◽

...

Keyword(s):

Deep Sea ◽

Environmental Water ◽

Comparative Genomic ◽

Acanthamoeba Polyphaga ◽

Deep Sea Sediment ◽

Worldwide Distribution ◽

The Family ◽

Genomic Analyses ◽

Giant Viruses ◽

Rats And Mice

The family Marseilleviridae was the second family of giant viruses that was described in 2013, after the family Mimiviridae. Marseillevirus marseillevirus, isolated in 2007 by coculture on Acanthamoeba polyphaga, is the prototype member of this family. Afterward, the worldwide distribution of marseilleviruses was revealed through their isolation from samples of various types and sources. Thus, 62 were isolated from environmental water, one from soil, one from a dipteran, one from mussels, and two from asymptomatic humans, which led to the description of 67 marseillevirus isolates, including 21 by the IHU Méditerranée Infection in France. Recently, five marseillevirus genomes were assembled from deep sea sediment in Norway. Isolated marseilleviruses have ≈250 nm long icosahedral capsids and 348–404 kilobase long mosaic genomes that encode 386–545 predicted proteins. Comparative genomic analyses indicate that the family Marseilleviridae includes five lineages and possesses a pangenome composed of 3,082 clusters of genes. The detection of marseilleviruses in both symptomatic and asymptomatic humans in stool, blood, and lymph nodes, and an up-to-30-day persistence of marseillevirus in rats and mice, raise questions concerning their possible clinical significance that are still under investigation.

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MICROPLASTIC IN THE DEEP-SEA SEDIMENT OF SOUTHWESTERN SUMATRAN WATERS

Marine Research in Indonesia ◽

10.14203/mri.v41i1.99 ◽

2016 ◽

Vol 41 (1) ◽

pp. 27-35 ◽

Cited By ~ 14

Author(s):

Muhammad Reza Cordova ◽

A'an J. Wahyudi

Keyword(s):

Indian Ocean ◽

Sea Level ◽

Deep Sea ◽

Plastic Waste ◽

Waste Plastic ◽

Deep Sea Sediment ◽

Sediment Samples ◽

Sampling Locations ◽

International Indian Ocean Expedition ◽

Marine Areas

Indonesia was recently ranked second on the list of countries producing plastic waste. Plastic can be degraded by thermal oxidation either with ultraviolet radiation and by mechanical to a very small size the size will be smaller. Degraded plastic with small sizes (<5 mm) measured has been micrometers known as microplastic. We took sediment samples on 07-18 May 2015 in EWIN 2015 cruise, which part of the contribution of Indonesian researchers for the International Indian Ocean Expedition-2 program, at 66.8 to 2182 m below sea level. Microplastic analysis from the sediment was carried out by using flotation methods. We found microplastic in 8 locations out of 10 sampling locations. We found 41 particles microplastic with a form of granules (35 particles) and fibers (6 particles). Most of microplastic particles were found at depths less than 500 m with 20 particles. The discovery of microplastic in the sediment from the sea of western Sumatra at a depth more than 2000 m, indicated that plastic, considered new developed materials (early nineteen centuries made), has invaded marine areas, including pristine areas. It confirms the statement that plastic waste has spread widely to different areas of the seas and oceans, including remote and mostly unknown areas such as the deep sea.

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