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1.
Environ Pollut ; 352: 124131, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38734049

ABSTRACT

Polyethylene terephthalate (PET) plastic pollution is widely found in deep-sea sediments. Despite being an international environmental issue, it remains unclear whether PET can be degraded through bioremediation in the deep sea. Pelagic sediments obtained from 19 sites across a wide geographic range in the Pacific Ocean were used to screen for bacteria with PET degrading potential. Bacterial consortia that could grow on PET as the sole carbon and energy source were found in 10 of the 19 sites. These bacterial consortia showed PET removal rate of 1.8%-16.2% within two months, which was further confirmed by the decrease of carbonyl and aliphatic hydrocarbon groups using attenuated total reflectance-Fourier-transform infrared analysis (ATR-FTIR). Analysis of microbial diversity revealed that Alcanivorax and Pseudomonas were predominant in all 10 PET degrading consortia. Meanwhile, Thalassospira, Nitratireductor, Nocardioides, Muricauda, and Owenweeksia were also found to possess PET degradation potential. Metabolomic analysis showed that Alcanivorax sp. A02-7 and Pseudomonas sp. A09-2 could turn PET into mono-(2-hydroxyethyl) terephthalate (MHET) even in situ stimulation (40 MPa, 10 °C) conditions. These findings widen the currently knowledge of deep-sea PET biodegrading process with bacteria isolates and degrading mechanisms, and indicating that the marine environment is a source of biotechnologically promising bacterial isolates and enzymes.


Subject(s)
Bacteria , Biodegradation, Environmental , Geologic Sediments , Polyethylene Terephthalates , Water Pollutants, Chemical , Polyethylene Terephthalates/metabolism , Pacific Ocean , Geologic Sediments/microbiology , Geologic Sediments/chemistry , Bacteria/metabolism , Bacteria/isolation & purification , Water Pollutants, Chemical/metabolism , Water Pollutants, Chemical/analysis , Seawater/microbiology , Pseudomonas/metabolism
2.
Front Microbiol ; 15: 1298781, 2024.
Article in English | MEDLINE | ID: mdl-38650873

ABSTRACT

Fungal diseases such as the devastating rice blast pose severe threats to crop production worldwide. Biological control of crop diseases caused by fungal pathogens is an environment-friendly approach for safeguarding crop production. But the insufficient availability of microbial agents effective against various fungal diseases has hampered the development of green production in crops. In this study, we identified a broad-spectrum antifungal bacterium, Streptomyces graminearus STR-1, showing antagonistic activity to diverse fungal pathogens including Magnaporthe oryzae, Rhizoctonia solani, Fusarium graminearum, Ustilaginoidea virens, and Bipolaris maydis. Its antifungal activity was relatively stable and less affected by temperature and pH. Evaluation of the biocontrol activity of STR-1 revealed that STR-1 prevented and controlled rice blast disease via eliciting plant immunity and suppressing fungal infection-structure development. STR-1 broth extract inhibited spore germination, likely through inhibiting protein synthesis. Combining LC-MS and chromatography analysis of the antimicrobial compounds purified from STR-1 broth extract, together with decoding STR-1 genomic sequence, we identified 4-oxo-4-[(1-phenylethyl)amino]but-2-enoic acid, 1,3,5-Trimethylpyrazole and SMA-1 as the potential main STR-1 secondary metabolites associated with its antifungal effects. This study suggests that bacterial strain STR-1 could be used for identifying highly effective and broad-spectrum secondary metabolites for containing rice blast and other crop diseases. The application of the active compounds offers a promising measure to tackle fungal disease.

3.
J Hazard Mater ; 465: 133339, 2024 Mar 05.
Article in English | MEDLINE | ID: mdl-38150757

ABSTRACT

Plastic waste released into the environments breaks down into microplastics due to weathering, ultraviolet (UV) radiation, mechanical abrasion, and animal grazing. However, little is known about the plastic fragmentation mediated by microbial degradation. Marine plastic-degrading bacteria may have a double-edged effect in removing plastics. In this study, two ubiquitous marine bacteria, Alcanivorax xenomutans and Halomonas titanicae, were confirmed to degrade polystyrene (PS) and lead to microplastic and nanoplastic generation. Biodegradation occurred during bacterial growth with PS as the sole energy source, and the formation of carboxyl and carboxylic acid groups, decreased heat resistance, generation of PS metabolic intermediates in cultures, and plastic weight loss were observed. The generation of microplastics was dynamic alongside PS biodegradation. The size of the released microplastics gradually changed from microsized plastics on the first day (1344 nm and 1480 nm, respectively) to nanoplastics on the 30th day (614 nm and 496 nm, respectively) by the two tested strains. The peak release from PS films reached 6.29 × 106 particles/L and 7.64 × 106 particles/L from degradation by A. xenomutans (Day 10) and H. titanicae (Day 5), respectively. Quantification revealed that 1.3% and 1.9% of PS was retained in the form of micro- and nanoplastics, while 4.5% and 1.9% were mineralized by A. xenomutans and H. titanicae at the end of incubation, respectively. This highlights the negative effects of microbial degradation, which results in the continuous release of numerous microplastics, especially nanoplastics, as a notable secondary pollution into marine ecosystems. Their fates in the vast aquatic system and their impact on marine lives are noted for further study.


Subject(s)
Polystyrenes , Water Pollutants, Chemical , Animals , Microplastics , Plastics , Ecosystem , Water Pollutants, Chemical/analysis , Biodegradation, Environmental
4.
Biotechnol Biofuels Bioprod ; 16(1): 169, 2023 Nov 06.
Article in English | MEDLINE | ID: mdl-37932798

ABSTRACT

BACKGROUND: Cottonseed oil is a promising edible plant oil with abundant unsaturated fatty acids. However, few studies have been conducted to explore the characteristics of cottonseed oil. The molecular mechanism of cottonseed oil accumulation remains unclear. RESULTS: In the present study, we conducted comparative transcriptome and weighted gene co-expression network (WGCNA) analysis for two G. hirsutum materials with significant difference in cottonseed oil content. Results showed that, between the high oil genotype 6053 (H6053) and the low oil genotype 2052 (L2052), a total of 412, 507, 1,121, 1,953, and 2,019 differentially expressed genes (DEGs) were detected at 10, 15, 20, 25, and 30 DPA, respectively. Remarkably, a large number of the down-regulated DEGs were enriched in the phenylalanine metabolic processes. Investigation into the dynamic changes of expression profiling of genes associated with both phenylalanine metabolism and oil biosynthesis has shed light on a significant competitive relationship in substrate allocation during cottonseed development. Additionally, the WGCNA analysis of all DEGs identified eight distinct modules, one of which includes GhPXN1, a gene closely associated with oil accumulation. Through phylogenetic analysis, we hypothesized that GhPXN1 in G. hirsutum might have been introgressed from G. arboreum. Overexpression of the GhPXN1 gene in tobacco leaf suggested a significant reduction in oil content compared to the empty-vector transformants. Furthermore, ten other crucial oil candidate genes identified in this study were also validated using quantitative real-time PCR (qRT-PCR). CONCLUSIONS: Overall, this study enhances our comprehension of the molecular mechanisms underlying cottonseed oil accumulation.

5.
Environ Microbiol ; 25(12): 2719-2731, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37421171

ABSTRACT

PET plastic waste entering the oceans is supposed to take hundreds of years to degrade and tends to accumulate in the deep sea. However, we know little about the bacteria capable of plastic degradation therein. To determine whether PET-degrading bacteria are present in deep-sea sediment, we collected the samples from the eastern central Pacific Ocean and initiated microbial incubation with PET as the carbon source. After enrichment with PET for 2 years, we gained all 15 deep-sea sediment communities at five oceanic sampling sites. Bacterial isolation for pure culture and further growth tests confirmed that diverse bacteria possess degradation ability including Alcanivorax xenomutans BC02_1_A5, Marinobacter sediminum BC31_3_A1, Marinobacter gudaonensis BC06_2_A6, Thalassospira xiamenensis BC02_2_A1 and Nocardioides marinus BC14_2_R3. Furthermore, four strains were chosen as representatives to reconfirm the PET degradation capability by SEM, weight loss and UPLC-MS. The results showed that after 30-day incubation, 1.3%-1.8% of PET was lost. De-polymerization of PET by the four strains was confirmed by the occurrence of the PET monomer of MHET and TPA as the key degradation products. Bacterial consortia possessing PET-degrading potential are prevalent and diverse and might play a key role in the removal of PET pollutants in deep oceans.


Subject(s)
Polyethylene Terephthalates , Tandem Mass Spectrometry , Polyethylene Terephthalates/metabolism , Chromatography, Liquid , Bacteria/metabolism , Biodegradation, Environmental
6.
Front Microbiol ; 14: 1177078, 2023.
Article in English | MEDLINE | ID: mdl-37362919

ABSTRACT

Verticillium dahliae (V. dahliae) is a notorious soil-borne pathogen causing Verticillium wilt in more than 400 dicotyledonous plants, including a wide range of economically important crops, such as cotton, tomato, lettuce, potato, and romaine lettuce, which can result in extensive economic losses. In the last decade, several studies have been conducted on the physiological and molecular mechanisms of plant resistance to V. dahliae. However, the lack of a complete genome sequence with a high-quality assembly and complete genomic annotations for V. dahliae has limited these studies. In this study, we produced a full genomic assembly for V. dahliae VD991 using Nanopore sequencing technology, consisting of 35.77 Mb across eight pseudochromosomes and with a GC content of 53.41%. Analysis of the genome completeness assessment (BUSCO alignment: 98.62%; Illumina reads alignment: 99.17%) indicated that our efforts resulted in a nearly complete and high-quality genomic assembly. We selected 25 species closely related to V. dahliae for evolutionary analysis, confirming the evolutionary relationship between V. dahliae and related species, and the identification of a possible whole genome duplication event in V. dahliae. The interaction between cotton and V. dahliae was investigated by transcriptome sequencing resulting in the identification of many genes and pathways associated with cotton disease resistance and V. dahliae pathogenesis. These results will provide new insights into the pathogenic mechanisms of V. dahliae and contribute to the cultivation of cotton varieties resistant to Verticillium wilt.

7.
J Hazard Mater ; 442: 130056, 2023 01 15.
Article in English | MEDLINE | ID: mdl-36183512

ABSTRACT

Plastics pollution poses a new threat to marine ecosystems. Mangrove locating at estuary worldwide is probably the most heavily polluted area trapping various plastics transported from terrestrial and nearby marine aquaculture. Expanded polystyrene (EPS) is one of most common plastic debris therein and even in the plastic garbage. Here we showed the bacterial diversity of the polystyrene-degrading microbial community from EPS waste sites from a subtropical mangrove area. After enrichment with EPS, the degradation consortia were obtained. They shared a similar community structure dominated by bacteria of Sphingomonadaceae, Rhodanobacteraceae, Rhizobiaceae, Dermacoccaceae, Rhodocyclaceae, Hyphomicrobiaceae, and Methyloligellaceae. Diverse bacteria standing for the first member of the genera of Novosphingobium, Gordonia, Stappia, Mesobacillus, Alcanivorax, Flexivirga, Cytobacillus, Thioclava, and Thalassospira showed PS degradation capability as a pure culture. Further, PS biodegradation of Gordonia sp. and Novosphingobium sp. was quantified by weight loss, in addition to obvious morphological and structural changes of the PS films observed by SEM, ATR-FTIR, and contact angle analysis. The formation of new oxygen-containing functional groups implied the degradation pathway of oxidation. Although the degradation rates ranged from 2.7% to 7.7% after one month in lab and possibly lower in situ, their role in EPS removal is unneglectable.


Subject(s)
Ecosystem , Polystyrenes , Polystyrenes/metabolism , Biodegradation, Environmental , Plastics/metabolism , Bacteria/metabolism , Oxygen/metabolism
8.
Article in English | MEDLINE | ID: mdl-35103584

ABSTRACT

Two novel Gram-stain-negative, aerobic, rod-shaped, carotenoid-pigmented and non-flagellated bacteria, designated BC31-1-A7T and BC31-3-A3T, were isolated from polyethylene-terephthalate-degrading bacterial consortia enriched from deep-sea sediment collected in the Pacific Ocean. Optimal growth of both strains was observed at 28-32 °C, at pH 7.5 and in the presence of 3-4% (w/v) NaCl. The 16S rRNA gene sequence analysis revealed that strains BC31-1-A7T and BC31-3-A3T were closely related to Muricauda aquimarina JCM 11811T, Muricauda lutimaris KCTC 22173T, Muricauda ruestringensis DSM 13258T, Muricauda zhangzhouensis DSM 25030T, Muricauda oceani JCM 33902T and Muricauda oceanensis KCTC 72200T with 96.8-98.9% sequence similarity. The 16S rRNA gene sequence similarity between strains BC31-1-A7T and BC31-3-A3T was 97.5%. The genomic G+C contents of strains BC31-1-A7T and BC31-3-A3T were 42.1 and 41.6 mol%, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain BC31-3-A3T, strain BC31-1-A7T and their six closely related type strains were 77.6-84.3% and 20.5-27.9%, respectively. Menaquinone-6 was detected as the major isoprenoid quinone in all strains. Their major fatty acids were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The major polar lipids of strains BC31-1-A7T and BC31-3-A3T were identified as one phosphatidylethanolamine, some unidentified polar lipids and one aminolipid. Based on their distinct taxonomic characteristics, strains BC31-1-A7T and BC31-3-A3T represent two novel species in the genus Muricauda. The names proposed to accommodate these two strains are Muricauda aurea sp. nov. and Muricauda profundi sp. nov., and the type strains are BC31-1-A7T (=MCCC M23246T=KCTC 82569T) and BC31-3-A3T (=MCCC M23216T=KCTC 82302T), respectively.


Subject(s)
Flavobacteriaceae/classification , Geologic Sediments/microbiology , Phylogeny , Seawater , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Flavobacteriaceae/isolation & purification , Nucleic Acid Hybridization , Pacific Ocean , Phospholipids/chemistry , Pigmentation , RNA, Ribosomal, 16S/genetics , Seawater/microbiology , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
9.
Front Microbiol ; 12: 755908, 2021.
Article in English | MEDLINE | ID: mdl-34745064

ABSTRACT

Members of the family Zoogloeaceae within the order Rhodocyclales are found to play vital roles in terrestrial and aquatic ecosystems by participating in biofloc formation in activated sludge, polycyclic aromatic hydrocarbon degradation, and nitrogen metabolism, such as denitrification and nitrogen fixation. Here, two bacterial strains designated H1-1-2AT and ZN11-R3-1 affiliated to the family Zoogloeaceae were isolated from coastal wetland habitats. The 16S rRNA gene sequences of the two strains were 100% identical and had maximum similarity with Nitrogeniibacter mangrovi M9-3-2T of 98.4% and ≤94.5% with other species. Phylogenetic analysis suggested that the two strains belonged to a single species and formed a novel monophyletic branch affiliated to the genus Nitrogeniibacter. The average nucleotide identity (ANI) value and digital DNA-DNA hybridization (dDDH) estimate between the two strains and N. mangrovi M9-3-2T were 78.5-78.7% and 21.4-21.6%, respectively, indicating that the two strains represent a novel species. The genomes of strain H1-1-2AT (complete genome) and ZN11-R3-1 (draft genome) were 4.7Mbp in length encoding ~4,360 functional genes. The DNA G+C content was 62.7%. Nitrogen fixation genes were found in the two strains, which were responsible for the growth on nitrogen-free medium, whereas denitrification genes found in N. mangrovi M9-3-2T were absent in the two strains. The respiratory quinone was ubiquinone-8. The major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and aminophospholipid. The major fatty acids were summed feature 3 (C16:1 ω7c and C16:1 ω6c), C16:0, C12:0, and C10:0 3-OH. Based on genomic, phenotypic, and chemotaxonomic characterizations, strains H1-1-2AT and ZN11-R3-1 represent a novel species of the genus Nitrogeniibacter, for which the name Nitrogeniibacter aestuarii sp. nov. is proposed. The type strain is H1-1-2AT (=MCCC 1K04284T=KCTC 82672T), and additional strain is ZN11-R3-1 (=MCCC 1A17971=KCTC 82671). Additionally, phylogenomic analysis of the members of the family Zoogloeaceae including type strains and uncultivated bacteria was performed, using the Genome Taxonomic Database toolkit (GTDB-Tk). Combined with the 16S rRNA gene phylogeny, four novel genera, Parazoarcus gen. nov., Pseudazoarcus gen. nov., Pseudothauera gen. nov., and Cognatazoarcus gen. nov., were proposed. This study provided new insights to the taxonomy of the family Zoogloeaceae.

10.
Article in English | MEDLINE | ID: mdl-33847553

ABSTRACT

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1-8 %, at pH 6.5-8 and at temperatures of 10-40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae, and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA-DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).


Subject(s)
Flavobacteriaceae/classification , Geologic Sediments/microbiology , Microbial Consortia , Phylogeny , Polyethylene Terephthalates/metabolism , Seawater/microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Flavobacteriaceae/isolation & purification , Pacific Ocean , Phospholipids/chemistry , Pigmentation , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
11.
IEEE/ACM Symp Edge Comput (2021) ; 2021: 94-105, 2021 Dec.
Article in English | MEDLINE | ID: mdl-37736032

ABSTRACT

Application latency requirements, privacy, and security concerns have naturally pushed computing onto smartphone and IoT devices in a decentralized manner. In response to these demands, researchers have developed micro-runtimes for WebAssembly (Wasm) on IoT devices to enable streaming applications to a runtime that can run the target binaries that are independent of the device. However, the migration of Wasm and the associated security research has neglected the urgent needs of access control on bare-metal, memory management unit (MMU)-less IoT devices that are sensing and actuating upon the physical environment. This paper presents Aerogel, an access control framework that addresses security gaps between the bare-metal IoT devices and the Wasm execution environment concerning access control for sensors, actuators, processor energy usage, and memory usage. In particular, we treat the runtime as a multi-tenant environment, where each Wasm-based application is a tenant. We leverage the inherent sandboxing mechanisms of Wasm to enforce the access control policies to sensors and actuators without trusting the bare-metal operating system. We evaluate our approach on a representative IoT development board: a cortex-M4 based development board (nRF52840). Our results show that Aerogel can effectively enforce compute resource and peripheral access control policies while introducing as little as 0.19% to 1.04% runtime overhead and consuming only 18.8% to 45.9% extra energy.

12.
Int J Syst Evol Microbiol ; 69(8): 2250-2257, 2019 Aug.
Article in English | MEDLINE | ID: mdl-31184574

ABSTRACT

A Gram-stain-negative, motile, non-spore-forming, aerobic and rod-shaped bacterial strain, Soil36-7T, was isolated from an in situ enriched hydrocarbon-degrading consortium in South China Sea sediment. Strain Soil36-7T grew at 4-40 °C (optimum 28-32 °C), at pH 5-10 (pH 7-8) and in the presence of 1-12 % (w/v) NaCl (3-6 %). Phylogenetic analyses based on 16S rRNA gene sequences and a genome-based approach using UBCGs (up-to-date bacterial core genes) showed Soil36-7T formed a distinct branching lineage within the family Alteromonadaceae. 16S rRNA gene sequence similarity was 92.9, 92.1 and >88.3 % between strain Soil36-7T and the type species of the genera Marinobacter, Tamilnaduibacter and the other genera of the family Alteromonadaceae, respectively. The major fatty acids in Soil36-7T were C16 : 0, C16 : 1ω6/7c, C16 : 0 10-methyl, C18 : 1ω7c, C12 : 0 and C18 : 0. The predominant respiratory quinone was Q-9, with a minor amount of Q-10 (3.5 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and various unidentified glycolipids, phospholipids, aminophospholipids and other polar lipids. The DNA G+C content was 57.9 mol%. On the basis of phylogenetic, genomic, phenotypic and chemotaxanomic characteristics, strain Soil36-7T could be classified as representing a novel species of a new genus within the family Alteromonadaceae, for which the name Hydrocarboniclastica marina gen. nov., sp. nov. is proposed. The type strain of the type species is Soil36-7T (=MCCC 1A12105T=KCTC 62334T).


Subject(s)
Alteromonadaceae/classification , Geologic Sediments/microbiology , Hydrocarbons/metabolism , Microbial Consortia , Phylogeny , Seawater/microbiology , Alteromonadaceae/isolation & purification , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Glycolipids/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
13.
Antonie Van Leeuwenhoek ; 112(5): 797-807, 2019 May.
Article in English | MEDLINE | ID: mdl-30600415

ABSTRACT

A taxonomic study was carried out on strain SA5d-4T, which was isolated from a marine limpet (Patelloida saccharina lanx [Reeve, 1855]) collected from intertidal rocks in Xiamen, China. Strain SA5d-4T was aerobic, Gram-positive, lacked flagellum, non-motile, filamentous, formed a slightly-yellowish colony, and non-sporulating. The strain grew optimally at 28 °C, at pH values 7.0-8.0, and in the presence of 1-2% (w/v) sodium chloride. The major cellular fatty acids identified were iso-C15:0, iso-C17:0ω10c, and iso-C17:0. The dominated respiratory quinone was menaquinone-7. The major phospholipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The genomic DNA G + C content was 35.3 mol%, calculated from a draft genome sequence. Phylogenetic analysis based on the full-length 16S rRNA gene sequence showed that strain SA5d-4T belongs to a new genus within the family Bacillaceae, and this gene shares 95.6% similarity with that from Bacillus taeanensis BH030017T, 95.2% with Bacillus algicola KMM 3737T, 95.1% with Bacillus alkalinitrilicus ANL-iso4T, 94.9% with Bacillus hwajinpoensis SW-72T, and 94.6% with Anaerobacillus alkalidiazotrophicus MS6T. Whole genome phylogenetic analyses indicated that strain SA5d-4T formed a monophyletic branch with B. taeanensis BH030017T. The average nucleotide identity between strain SA5d-4T and B. taeanensis BH030017T was 69.6%. Based on polyphasic taxonomic characteristics, strain SA5d-4T represents a novel species of a new genus, for which the name Lottiidibacillus patelloidae gen. nov., sp. nov., is proposed with the type strain SA5d-4T (= MCCC 1A11654T = KCTC 33831T). Based on phylogenetic analyses, B. taeanensis should be transferred to a new genus, named Maribacillus, as Maribacillus taeanensis comb. nov., with type strain BH030017T (= KCTC 3918T = DSM 16466T).


Subject(s)
Bacillaceae/classification , Bacillus/classification , Gastropoda/microbiology , Intestines/microbiology , Animals , Bacillaceae/genetics , Bacillaceae/isolation & purification , Bacillaceae/metabolism , Bacillus/genetics , Bacillus/isolation & purification , Bacillus/metabolism , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Fatty Acids/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics
14.
Antonie Van Leeuwenhoek ; 112(3): 425-434, 2019 Mar.
Article in English | MEDLINE | ID: mdl-30302650

ABSTRACT

A piezotolerant, cold-adapted, slightly halophilic bacterium, designated strain PWS21T, was isolated from a deep-sea sediment sample collected from the New Britain Trench. Cells were observed to be Gram-stain negative, rod-shaped, oxidase- and catalase-positive. Growth of the strain was observed at 4-45 °C (optimum 37 °C), at pH 5.0-9.0 (optimum 7.0) and in 0.5-20% (w/v) NaCl (optimum 3-4%). The optimum pressure for growth was 0.1 MPa (megapascal) with tolerance up to 70 MPa. 16S rRNA gene sequence analysis showed that strain PWS21T is closely related to Marinobacter guineae M3BT (98.4%) and Marinobacter lipolyticus SM19T (98.2%). Multilocus sequence analysis (MLSA) based on sequences of housekeeping genes gyrB, recA, atpD, rpoB and rpoD indicates that strain PWS21T represents a distinct evolutionary lineage within the genus Marinobacter. Furthermore, strain PWS21T showed low ANI and diDDH values to the closely related species. The principal fatty acids were identified as C12:0, C12:0 3-OH, C16:1ω9c, C16:0 and C18:1ω9c. Ubiquinone-9 was identified as the major respiratory quinone. The polar lipids were identified as phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), aminophospholipid (APL), two unidentified lipids and an unidentified phospholipid (PL). The G + C content of the genomic DNA was determined to be 60.3 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, we conclude that strain PWS21T represents a novel species of the genus Marinobacter, for which the name Marinobacter profundi sp. nov. is proposed (type strain PWS21T = KCTC 52990T = MCCC 1K03345T).


Subject(s)
Geologic Sediments/microbiology , Marinobacter/classification , Marinobacter/isolation & purification , Base Composition , Cluster Analysis , Cytosol/chemistry , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Enzymes/analysis , Fatty Acids/analysis , Hydrogen-Ion Concentration , Hydrothermal Vents/microbiology , Marinobacter/genetics , Marinobacter/physiology , Multilocus Sequence Typing , Pacific Ocean , Phospholipids/analysis , Phylogeny , Quinones/analysis , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Sodium Chloride/metabolism , Temperature
15.
Int J Syst Evol Microbiol ; 68(9): 2943-2948, 2018 Sep.
Article in English | MEDLINE | ID: mdl-30028290

ABSTRACT

Two novel marine bacteria, designated strains CSC3H3T and CSC1P2, were isolated from surface seawater of the South China Sea. Both strains were Gram-negative, oxidase-positive, catalase-positive, curved rods and motile. They grew at 10-40 °C, pH 5-10 and in the presence of 0-15 % (w/v) NaCl. Their 16S rRNA gene sequences were identical to each other. Phylogenetic analysis based on 16S rRNA gene sequences indicated that they belong to the genus Thalassospira, and shared 97.5-98.3 % sequence similarity to all other validly type strains of the genus Thalassospira, and the highest similarity was to the type strain Thalassospira povalilyticaZumi 95T (98.3 %), followed by Thalassospira australica NP3b2T (98.2 %). The digital DNA-DNA hybridization value between the two strains was 80.4 %, while the values with T. povalilyticaZumi 95T and T. australica NP3b2T were only 20.5-20.7 % and 20.4-20.5 %, respectively. The two strains possess similar major cellular fatty acids including C18 : 1ω7c, C16 : 0, C19 : 0ω8c cyclo, C18 : 1 2-OH and C17 : 0 cyclo. The G+C contents of the chromosomal DNA of strains CSC3H3T and CSC1P2 were 54.6 and 54.5 mol%, respectively. The major respiratory quinone was ubiquinone 10. Phosphatidylethanolamine, phosphatidylglycerol and several unidentified phospholipids, aminolipid and lipids were present in both strains. Based on phenotypic and genotypic characteristics, the two strains represent a novel species within the genus Thalassospira, for which the name Thalassospira marina sp. nov. is proposed. The type strain is CSC3H3T (=MCCC 1A11786T=KCTC 62333T).


Subject(s)
Phylogeny , Rhodospirillaceae/classification , Seawater/microbiology , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Rhodospirillaceae/genetics , Rhodospirillaceae/isolation & purification , Sequence Analysis, DNA , Ubiquinone/chemistry
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