scholarly journals Bacterial Vegetative Insecticidal Proteins (Vip) from Entomopathogenic Bacteria

2016 ◽  
Vol 80 (2) ◽  
pp. 329-350 ◽  
Author(s):  
Maissa Chakroun ◽  
Núria Banyuls ◽  
Yolanda Bel ◽  
Baltasar Escriche ◽  
Juan Ferré
Keyword(s):  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Bt Cotton ◽  
Cry Proteins ◽  
Insecticidal Proteins ◽  
Proteolytic Activation ◽  
Content Type ◽  
Entomopathogenic Bacteria ◽  
Vip Proteins ◽  
Parasporal Crystals

SUMMARYEntomopathogenic bacteria produce insecticidal proteins that accumulate in inclusion bodies or parasporal crystals (such as the Cry and Cyt proteins) as well as insecticidal proteins that are secreted into the culture medium. Among the latter are the Vip proteins, which are divided into four families according to their amino acid identity. The Vip1 and Vip2 proteins act as binary toxins and are toxic to some members of the Coleoptera and Hemiptera. The Vip1 component is thought to bind to receptors in the membrane of the insect midgut, and the Vip2 component enters the cell, where it displays its ADP-ribosyltransferase activity against actin, preventing microfilament formation. Vip3 has no sequence similarity to Vip1 or Vip2 and is toxic to a wide variety of members of the Lepidoptera. Its mode of action has been shown to resemble that of the Cry proteins in terms of proteolytic activation, binding to the midgut epithelial membrane, and pore formation, although Vip3A proteins do not share binding sites with Cry proteins. The latter property makes them good candidates to be combined with Cry proteins in transgenic plants (Bacillus thuringiensis-treated crops [Bt crops]) to prevent or delay insect resistance and to broaden the insecticidal spectrum. There are commercially grown varieties of Bt cotton and Bt maize that express the Vip3Aa protein in combination with Cry proteins. For the most recently reported Vip4 family, no target insects have been found yet.

scholarly journals Salinibaculum litoreum gen. nov., sp. nov., isolated from salted brown alga Laminaria

2020 ◽  
Vol 70 (4) ◽  
pp. 2879-2887 ◽  
Author(s):  
Dong Han ◽  
Heng-Lin Cui
Keyword(s):  
Brown Alga ◽  
Type Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
A Minor

A novel Gram-stain-negative, aerobic and rod-shaped halophilic archaeon, designated HD8-45T, was isolated from the red brine of salted brown alga Laminaria produced at Dalian, PR China. According to the results of 16S rRNA gene and rpoB′ gene sequence comparisons, strain HD8-45T showed the highest sequence similarity to the corresponding genes of Salinirussus salinus YGH44T (95.1 and 85.2 % similarities, respectively), Halovenus aranensis EB27T (91.2 and 86.0 % similarities, respectively). The low sequence similarity and the phylogeny implied the novel generic status of strain HD8-45T. Genomic relatedness analyses showed that strain HD8-45T were clearly distinguished from other species in the order Halobacteriales , with average nucleotide identity, amino acid identity and in silico DNA–DNA hybridization values not more than 75.1, 65.6 and 21.5 %. The polar lipid pattern contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two major glycolipids and two minor glycolipids. The two major glycolipids and a minor glycolipid were chromatographically identical to disulfated mannosyl glucosyl diether, sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. The major respiratory quinones were menaquinone MK-8 and MK-8(H2). The DNA G+C content was 62.0 mol% (Tm ) and 61.9 mol% (genome). All these results showed that strain HD8-45T represents a novel species of a new genus in the order Halobacteriales , for which the name Salinibaculum litoreum gen. nov., sp. nov. is proposed. The type strain of Salinibaculum litoreum is HD8-45T (=CGMCC 1.15328T=JCM 31107T).

Acerihabitans arboris gen. nov., sp. nov., a new member of the family Pectobacteriaceae isolated from sap drawn from Acer pictum

2021 ◽  
Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Hanna Choe ◽  
Ji-Sun Kim
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-negative, facultatively anaerobic bacterium, designated SAP-6T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea and its precise taxonomic status was determined by a polyphasic approach. Cells were non-sporulating, motile, short rods and showed growth at 4–37 °C, pH 6.0–8.0 and 0–4% NaCl. Phylogenomic analysis based on 92 core gene sequences showed that strain SAP-6T belonged to the family Pectobacteriaceae and formed a distinct clade between members of the genera Sodalis and Biostraticola with gene support index of 89. The closest phylogenetic neighbours were Biostraticola tofi DSM 19580T (97.3% 16S rRNA gene sequence similarity) and Sodalis praecaptivus HS1T (96.8%), with the average amino acid identity values of 75.3% and 74.0%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The major isoprenoid quinones were Q-7 and Q-8. The predominant fatty acids were C16:0, C17:0 cyclo and summed feature 3. The DNA G+C content was 57.0%. On the basis of data presented here, strain SAP-6T (=KCTC 52622T=DSM 104038T) represents a novel species of a new genus in the family Pectobacteriaceae , for which the name Acerihabitans arboris gen. nov., sp. nov. is proposed.

scholarly journals Genome-based analyses reveal the presence of 12 heterotypic synonyms in the genus Streptomyces and emended descriptions of Streptomyces bottropensis, Streptomyces celluloflavus, Streptomyces fulvissimus, Streptomyces glaucescens, Streptomyces murinus, and Streptomyces variegatus

2020 ◽  
Vol 70 (6) ◽  
pp. 3924-3929 ◽  
Author(s):  
Munusamy Madhaiyan ◽  
Venkatakrishnan Sivaraj Saravanan ◽  
Wah-Seng See-Too
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Genus Streptomyces ◽  
Content Type ◽  
Link Type ◽  
Streptomyces Glaucescens

Phylogenetic analysis based on 16S rRNA gene sequences of the genus Streptomyces showed the presence of six distinguishable clusters, with 100 % sequence similarity values among strains in each cluster; thus they shared almost the same evolutionary distance. This result corroborated well with the outcome of core gene (orthologous gene clusters) based genome phylogeny analysis of 190 genomes including the Streptomyces species in those six clusters. These preeminent results led to an investigation of genome-based indices such as digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) for the strains in those six clusters. Certain strains recorded genomic indices well above the threshold values (70 %, 95–96 % and >95 % for dDDH, ANI and AAI, respectively) determined for species affiliation, suggesting only one type strain belongs to described species and the other(s) may need to be reduced in taxa to a later heterotypic synonym. To conclude, the results of comprehensive analyses based on phylogenetic and genomic indices suggest that the following six reclassifications are proposed: Streptomyces flavovariabilis as a later heterotypic synonym of Streptomyces variegatus ; Streptomyces griseofuscus as a later heterotypic synonym of Streptomyces murinus ; Streptomyces kasugaensis as a later heterotypic synonym of Streptomyces celluloflavus ; Streptomyces luridiscabiei as a later heterotypic synonym of Streptomyces fulvissimus ; Streptomyces pharetrae as a later heterotypic synonym of Streptomyces glaucescens ; and Streptomyces stelliscabiei as a later heterotypic synonym of Streptomyces bottropensis .

Jannaschia marina sp. nov., isolated from the gut of a gastropod, Onchidium reevesii

2021 ◽  
Author(s):  
Si Chen ◽  
Mengyuan He ◽  
Qiliang Lai ◽  
Ying Xu ◽  
Chenjing Shang
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Phenotypic Data ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A taxonomic study was carried out on strain SHC163T, which was isolated from the gut of Onchidium reevesii. The bacterium was Gram-stain-negative, oxidase-positive, catalase-negative and rod-shaped. Growth was observed at salinities of 0–4.0 % NaCl and at temperatures of 15–35 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SHC163T belonged to the genus Jannaschia , with the highest sequence similarity to Jannaschia seosinensis CL-SP26T (97.9%), followed by Jannaschia faecimaris DSM 100420T (97.8 %), Jannaschia rubra CECT 5088T (97.5%) and eight species of the genus Jannaschia (94.7−97.1 %). The average amino acid identity, average nucleotide identity and the digital DNA–DNA hybridization estimate values between strain SHC163T and the type strains of the genus Jannaschia were 64.33−79.78 %, 71.0−78.4 % and 19.2−21.0%, respectively. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c, 56.5 %), C18 : 1  ω7c 11-methyl (23.1 %), C18 : 0 (8.7 %). The G+C content of the chromosomal DNA was 67.8 mol%. The respiratory quinone was determined to be Q-10 (100 %). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and aminophospholipid. The combined genotypic and phenotypic data show that strain SHC163T represents a novel species within the genus Jannaschia , for which the name Jannaschia marina sp. nov. is proposed, with the type strain SHC163T (=MCCC 1K04032T=KCTC 72524T).

Novisyntrophococcus fermenticellae gen. nov., sp. nov., isolated from an anaerobic fermentation cellar of Chinese strong-flavour baijiu

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Li-Juan Chai ◽  
Guan-Yu Fang ◽  
Peng-Xiang Xu ◽  
Xiao-Juan Zhang ◽  
Zhen-Ming Lu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
Anaerobic Fermentation ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Novel Genus And Species

A Gram-stain-negative, coccus-shaped, obligately anaerobic, non-motile and non-spore-forming bacterium, designated strain JN500902T, was isolated from the mud in a fermentation cellar used continuously over 30 years for Chinese strong-flavour baijiu production. Colonies were white, circular, convex and smooth-edged. Growth was observed at 20–40 °C (optimum, 37 °C), at pH 5.0–10 (optimum, pH 7.5), with 0–2 % (w/v) NaCl and with 0–4 % (v/v) ethanol. The Biolog assay demonstrated positive reactions of strain JN500902T in the metabolism of l-fucose and pyruvate. The predominant cellular fatty acids (>10 %) consisted of C16 : 0 and C14 : 0. The major end metabolites of strain JN500902T were acetic acid and ethanol when incubated anaerobically in liquid reinforced clostridial medium. Acetate was the major organic acid end product. The complete genome size of strain JN500902T was 3 420 321 bp with 3327 identified genes. The G+C content was 43.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain JN500902T with the family Lachnospiraceae , having low sequence similarity (92.8 %) to the nearest type strain, Syntrophococcus sucromutans DSM 3224T and forming a clearly distinct branch. Core genome phylogenetic analysis of the isolate and 134 strains belonging to the family Lachnospiraceae also revealed that strain JN500902T was well-separated from other genera of this family as a monophyletic clade. The average nucleotide identity and amino acid identity values between strain JN500902T and 134 Lachnospiraceae strains were less than 74 and 65 %, respectively. Considering its polyphasic characteristics, strain JN500902T represents a novel genus and species within the family Lachnospiraceae , for which the name Novisyntrophococcus fermenticellae gen. nov., sp. nov. is proposed. The type strain is JN500902T (=CICC 24502T=JCM 33939T).

scholarly journals Marinicella rhabdoformis sp. nov., isolated from coastal sediment

2020 ◽  
Vol 70 (5) ◽  
pp. 3528-3533 ◽  
Author(s):  
Yan-lin Zhong ◽  
Xun-Ke Sun ◽  
Jian-Gang Hui ◽  
Hui-ling Teng ◽  
Zong-Jun Du
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Amino Acid Identity ◽  
Coastal Sediment ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Pr China

A Gram-stain-negative, rod-shaped, facultative anaerobic bacterium, designated strain 3539T, was isolated from coastal sediment of Weihai, PR China. Optimal growth occurred at 28 °C, pH 7.5–8.0 and in the presence of 3.0 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 3539T formed a robust clade with members of the genus Marinicella and was closely related to Marinicella litoralis JCM 16154T, Marinicella sediminis F2T and Marinicella pacifica sw153T with 97.7, 96.2 and 95.4 % sequence similarity, respectively. The average amino acid identity, percentage of conserved proteins, average nucleotide identity and digital DNA–DNA hybridization values between strain 3539T and M. litoralis JCM 16154T were 64.9, 68.3, 72.8 and 18.9 %, respectively. The genomic DNA G+C content of strain 3539T was 42.0 mol%. The dominant respiratory quinone was ubiquinone-8, and the major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c). The polar lipids of strain 3539T consisted of phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified lipid and three unidentified phospholipids. Based on the combination of phylogenetic, phenotypic and chemotaxonomic data, strain 3539T is considered to represent a novel species within the genus Marinicella in he family Alcanivoracaceae , for which the name Marinicella rhabdoformis sp. nov. is proposed. The type strain of the new species is 3539T (=KCTC 72414T=MCCC 1H00388T).

Description of Acinetobacter kanungonis sp. nov., based on phylogenomic analysis

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Lipika Das ◽  
Sushanta Deb ◽  
Subrata K. Das
Keyword(s):  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Cellular Components ◽  
Reference Strains ◽  
Type Strains

A novel strain of a member of the genus Acinetobacter, strain PS-1T, was isolated from the skin of fresh water pufferfish (Tetraodon cutcutia) collected from Mahanadi River, India. Cells were Gram-stain-negative, aerobic, coccoid and non-motile. The predominant polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and phospholipid (PL) and the cell wall sugars were glucose, galactose and ribose. The major cellular fatty acids of PS-1T were C18 : 1ω9c (30.67 %), C16 : 1ω7c (19.54 %), C16 : 0 (15.87 %), C12 : 0 (7.35 %) and C12 : 0 3-OH (6.77 %). The genome size was 3.5 Mbp and the DNA G+C content was 41.97 %. Gene ontology study revealed that the major fraction of genes were associated with biological processes (53.99 %) followed by molecular function (30.42 %) and cellular components (15.58 %). Comparisons of 16S rRNA gene sequences revealed 97.94–97.05 % sequence similarity with the closely related type strains of species of the genus Acinetobacter . The average nucleotide identity (ANI) and average amino acid identity (AAI) of PS-1T with reference strains of species of the genus Acinetobacter with validly published names were bellow 95–96 and the corresponding in-silico DNA–DNA hybridization (DDH) values were below 70 %. A phylogenomic tree based on core genome analysis supported these results. Genotypic and phenotypic characteristics of PS-1T indicate that the strain represents a novel species of the genus Acinetobacter and the name Acinetobacter kanungonis sp. nov. is proposed. The type strain is PS-1T (=JCM 34131T=NCIMB 15260T)

scholarly journals Duganella callida sp. nov., a novel addition to the Duganella genus, isolated from the soil of a cultivated maize field

2020 ◽  
Author(s):  
Rachel Raths ◽  
Vincent Peta ◽  
Heike Bücking
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Maize Field ◽  
Identity Score ◽  
Bacterium Strain

A Gram-negative, rod-shaped bacterium, strain Duganella callida DN04T, was isolated from the soil of a maize field in North Carolina, USA. Based on the 16S rRNA gene sequence, the most similar Duganella species are D. sacchari Sac-22T, D. ginsengisoli DCY83T, and D. radicis Sac-41T with a 97.8, 97.6, or 96.9 % sequence similarity, respectively. We compared the biochemical phenotype of DN04T to D. sacchari Sac-22T and D. zoogloeoides 115T and other reference strains from different genera within the Oxalobacteraceae and while the biochemical profile of DN04T is most similar to D. sacchari Sac-22T and other Duganella and Massilia strains, there are also distinct differences. DN04T can for example utilize turanose, N-acetyl-d-glucosamine, inosine, and l-pyroglutamic acid. The four fatty acids found in the highest percentages were C15 : 0 iso (24.6 %), C15 : 1 isoG (19.4 %), C17 : 0 iso3-OH (16.8 %), and summed feature 3 (C16:1 ⍵7c and/or C16:1 ⍵6c) (12.5 %). We also applied whole genome sequencing to determine if DN04T is a novel species. The most similar AAI (average amino acid identity) score was 70.8 % ( Massilia plicata NZ CP038026T), and the most similar ANI (average nucleotide identity) score was 84.8 % ( D. radicis KCTC 22382T), which indicates that DN04T is a novel species. The genome-to-genome-distance calculation (GGDC) revealed a DDH of 28.3 % to D. radicis KCTC 22382T, which is much lower than the new species threshold. Based on the morphological, phenotypic, and genomic differences, we propose Duganella callida sp. nov. as a novel species within the Duganella genus (type strain DN04T=NRRL B-65552T=LMG 31736T).

scholarly journals Reclassification of Sphingomonas aeria as a later heterotypic synonym of Sphingomonas carotinifaciens based on whole-genome sequence analysis

2020 ◽  
Vol 70 (4) ◽  
pp. 2355-2358 ◽  
Author(s):  
Munusamy Madhaiyan ◽  
Venkatakrishnan Sivaraj Saravanan ◽  
Joseph S. Wirth ◽  
William B. Whitman
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
Conserved Genes ◽  
Taxonomic Assignments

The 16S rRNA gene sequences of Sphingomonas carotinifaciens L9-754T and Sphingomonas aeria B093034T possess 99.71 % sequence similarity. Further studies were undertaken to clarify the taxonomic assignments of these species. Whole-genome comparisons showed that S. aeria B093034Tand S. carotinifaciens L9-754T shared 96.9 % average nucleotide identity, 98.4 % average amino acid identity and 76.1 % digital DNA–DNA hybridization values. These values exceeded or approached the recommended species delineation threshold values. Furthermore, a phylogenetic tree based on 41 of the most conserved genes provided additional evidence that S. aeria B093034T and S. carotinifaciens L9-754T are very closely related. Based on this evidence we propose the reclassification of S. aeria Xue et al. 2018 as a later heterotypic synonym of S. carotinifaciens Madhaiyan et al. 2017.

scholarly journals Mesonia oceanica sp. nov., isolated from oceans during the Tara oceans expedition, with a preference for mesopelagic waters

2020 ◽  
Vol 70 (7) ◽  
pp. 4329-4338 ◽  
Author(s):  
Teresa Lucena ◽  
Isabel Sanz-Sáez ◽  
David R. Arahal ◽  
Silvia G. Acinas ◽  
Olga Sánchez ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

Strain ISS653T, isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bacterium, strictly aerobic and chemoorganotrophic, slightly halophilic (1–15 % NaCl) and mesophilic (4–37 °C), oxidase- and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C15 : 0, iso-C15 : 0 2-OH, and iso-C17 : 0 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family Flavobacteriaceae, with the type strains of Mesonia phycicola (93.2 %), Salegentibacter mishustinae (93.1 %) and Mesonia mobilis (92.9 %) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with M. mobilis (81 % AAI; 78.9 % ANI), M. phycicola (76 % AAI; 76.3 % ANI), Mesonia maritima (72 % AAI, 74.9 % ANI), Mesonia hippocampi (64 % AAI, 70.8 % ANI) and Mesonia algae (68 % AAI; 72.2 % ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653T in a clade with species of the genus Mesonia . We conclude that strain ISS653T represents a novel species of the genus Mesonia for which we propose the name Mesonia oceanica sp. nov., and strain ISS653T (=CECT 9532T=LMG 31236T) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the Tara oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans.

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