Three Novel Marine Species of Paracoccus, P. aerodenitrificans sp. nov., P. sediminicola sp. nov. and P. albus sp. nov., and the Characterization of Their Capability to Perform Heterotrophic Nitrification and Aerobic Denitrification

Heterotrophic nitrification-aerobic denitrification (HN-AD) is an efficient nitrogen removal process and the genus Paracoccus is one important group of the HN-AD bacteria. During an investigation of the microbial diversity in marine ranching of the Pearl River Estuary (PR China), three bacterial strains, designated SCSIO 75817^T, SCSIO 76264^T and SCSIO 80058^T, were isolated from sediments. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the three strains belonged to the genus Paracoccus and their closest neighbors were P. isoporae DSM 22220^T (97.6-98.0%), P. aurantiacus CGMCC 1.13898^T (97.3-97.6%) and P. xiamenensis MCCC 1A16381^T (97.1-97.4%), respectively. The analysis results of 16S rRNA gene similarity, ANI, AAI and dDDH showed that the pairwise similarities between these three strains and their closest neighbors were 97.4-98.5%, 76.9-81.0%, 75.5-79.6% and 20.3-23.3%, respectively. Polyphasic taxonomic data of the phylogenetic, phenotypic and chemotaxonomic analyses indicate that these strains represent three novel species in the genus Paracoccus, for which the names Paracoccus aerodenitrificans sp. nov., Paracoccus sediminicola sp. nov. and Paracoccus albus sp. nov. are proposed, respectively. The study also demonstrated the heterotrophic nitrification-aerobic denitrification (HN-AD) ability of the novel species P. aerodenitrificans SCSIO 75817^T. When it was aerobically cultivated at 28 °C using NH₄⁺-N, NO₃^--N and NO₂^--N as the sole nitrogen sources, the nitrogen removal efficiencies were 73.4, 55.27 and 49.2%, respectively, and the maximum removal rates were 3.05, 1.82 and 1.63 mg/L/h, respectively. The results suggest that it has promising potential for wastewater treatment.

Polyphasic Characterization of Four Aspergillus Species as Potential Biocontrol Agents for White Mold Disease of Bean

The genus Aspergillus comprises several species that play pivotal roles in agriculture. Herein, we morphologically and physiologically characterized four genetically distinct Aspergillus spp., namely A. japonicus, A. niger, A. flavus, and A. pseudoelegans, and examined their ability to suppress the white mold disease of bean caused by Sclerotinia sclerotiorum in vitro and under greenhouse conditions. Seriation type of Aspergillus spp. correlates with conidiospores discharge as detected on the Petri glass lid. Members of Nigri section cover their conidial heads with hard shells after prolonged incubation. In addition, sporulation of the tested Aspergillus isolates is temperature sensitive as it becomes inhibited at low temperatures and the colonies become white. Examined Aspergillus spp. were neither infectious to legumes nor aflatoxigenic as confirmed by HPLC except for A. flavus and A. pseudoelegans which, secreted 5 and 1 ppm of aflatoxin B1, respectively. Co-inoculations of Sclerotinia’s mycelium or sclerotia with a spore suspension of Aspergillus spp. inhibited their germination on PDA at 18 °C and 28 °C, and halted disease onset on detached common bean and soybean leaves. Similarly, plants treated with A. japonicus and A. niger showed the highest survival rates compared to untreated plants. In conclusion, black Aspergillus spp. are efficient biocides and safe alternatives for the management of plant diseases, particularly in organic farms.

Caenimonas aquaedulcis sp. nov., Isolated from Freshwater of Daechung Reservoir during Microcystis Bloom

A Gram-stain-negative, white-coloured, and rod-shaped bacterium, strain DR4-4^T, was isolated from Daechung Reservoir, Republic of Korea, during Microcystis bloom. Strain DR4-4^T was most closely related to Caenimonas terrae SGM1-15^T and Caenimonas koreensis EMB320^T with 98.1% 16S rRNA gene sequence similarities. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain DR4-4^T and closely related type strains were below 79.46% and 22.30%, respectively. The genomic DNA G+C content was 67.5%. The major cellular fatty acids (≥10% of the total) were identified as C_16:0, cyclo C_17:0, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). Strain DR4-4^T possessed phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol as the main polar lipids and Q-8 as the respiratory quinone. The polyamine profile was composed of putrescine, cadaverine, and spermidine. The results of polyphasic characterization indicated that the isolated strain DR4-4^T represents a novel species within the genus Caenimonas, for which the name Caenimonas aquaedulcis sp. nov. is proposed. The type strain is DR4-4^T (=KCTC 82470^T =JCM 34453^T).

Cochlodiniinecator piscidefendens gen. nov., sp. nov., an algicidal bacterium against the ichthyotoxic dinoflagellate Cochlodinium polykrikoides

Harmful algal blooms caused by Cochlodinium polykrikoides result in enormous economic damage to the aquaculture industry. Biological control methods have attracted wide attention due to their environmental-friendliness. In this study, a novel algicidal bacterium, designated strain M26A2M^T, was determined for its taxonomic position and was evaluated for its potential to mitigate C. polykrikoides blooms. Strain M26A2M^T exhibited the highest 16S rRNA gene sequence similarity to the type strains of Planktotalea lamellibrachiae (97.3%), Halocynthiibacter namhaensis (97.2%), Pseudohalocynthiibacter aestuariivivens (96.8%) and Halocynthiibacter arcticus (96.4%) in the family Rhodobacteraceae. The predominant fatty acids were C_{10 : 0} 3-OH and summed feature 8 (comprising C_{18 : 1} ω7c and/or C_{18 : 1} ω6c). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Q-10 was the respiratory quinone. Strain M26A2M^T exerted significant algicidal activity against C. polykrikoides cells by destroying the membrane integrity and the photosynthetic system. Our findings suggest that strain M26A2M^T shows a high potential to control outbreaks of C. polykrikoides. Based on the polyphasic characterization, strain M26A2M^T is considered to represent a novel species within a novel genus of the family Rhodobacteraceae, for which the name Cochlodiniinecator piscidefendens gen. nov., sp. nov. is proposed. The type strain is M26A2M^T (=KCTC 82083^T=JCM 34119^T).

Mariniflexile maritimum sp. nov., isolated from seawater of the South Sea in the Republic of Korea

A novel Gram-stain-negative, rod-shaped, aerobic, non-motile bacterial strain, designated M5A1M^T, was isolated from seawater collected from the South Sea of the Republic of Korea. Based on 16S rRNA gene sequence similarity, strain M5A1M^T was closely related to Mariniflexile gromovii KMM 6038^T (95.3 %), Mariniflexile fucanivorans SW5^T (95.2 %), Mariniflexile soesokkakense RSSK-9^T (95.1 %), Yeosuana aromativorans GW1-1^T (94.6 %) and Confluentibacter lentus HJM-3^T (94.6 %). Genome-based phylogenetic analyses revealed that strain M5A1M^T formed a distinct cluster with the type strains of the genus Mariniflexile. The major cellular fatty acid constituents (>5 % of the total fatty acids) were iso-C_15:0, anteiso-C_15 : 0, iso-C_15 : 0 3-OH, iso-C_15 : 1 G, iso-C_16:03-OH and iso-C_17 : 0 3-OH. The respiratory quinone was identified as MK-6. The major polar lipids were phosphatidylethanolamine and one unidentified polar lipid. The genomic DNA G+C content of strain M5A1M^T was determined to be 37.7 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain M5A1M^T is considered to represent a novel species within the genus Mariniflexile, for which the name Mariniflexile maritimum sp. nov. is proposed. The type strain is M5A1M^T (=KCTC 72895^T=JCM 33982^T).

Novosphingobium aquimarinum sp. nov., isolated from seawater

A novel Gram-stain-negative, aerobic, and rod-shaped bacterial strain, M24A2M^T, was isolated from seawater in the Republic of Korea. On the basis of the 16S rRNA gene phylogeny, strain M24A2M^T was found to be closely related to Novosphingobium pentaromativorans US6-1^T and Novosphingobium mathurense SM117^T with pair-wise sequence similarities of 97.4 and 96.9 %, respectively. Phylogenetic analysis of 16S rRNA sequences indicated that M24A2M^T formed a branch with Novosphingobium pentaromativorans US6-1^T and represented a member of the genus Novosphingobium. The predominant cellular fatty acids were C_14 : 0 2-OH, summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c), and summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c). The polar lipids of strain M24A2M^T consisted mainly of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid, and two unidentified lipids. The respiratory quinone was ubiquinone Q-10. The genomic DNA G+C content was 63.9 %. Given the phenotypic characteristics along with the phylogenetic distinctness and chemotaxonomic features, strain M24A2M^T is considered to represent a novel species within the genus Novosphingobium, for which the name Novosphingobium aquimarinum sp. nov. is proposed. The type strain of Novosphingobium aquimarinum sp. nov. is M24A2M^T (=KCTC 72894^T=JCM 33983^T).

Flavobacterium amnigenum sp. nov. Isolated from a River

A yellowish, flexirubin-pigment-producing strain I3-3^T was isolated from river water in Iksan, the Republic of Korea. The strain was gram-negative, aerobic, non-motile, showed catalase and oxidase activities, and could grow at a temperature range of 10-35°C, pH 5.0-10 and 0-2.0% (w/v) of NaCl. The major fatty acids were iso-C_15:0, iso-C_17:0 3-OH and summed feature 3 (comprising C_16:1ω7c and/or C_16:1ω6c). The isolate contained phosphatidylethanolamine, one aminolipid, and two unidentified lipids as the major polar lipids. Menaquinone-6 (MK6) was the major respiratory quinone. The G+C content of the genomic DNA of strain I3-3^T was 35.6%. Comparison of the 16S rRNA gene sequence with the sequences of the closely related type strains showed highest sequence similarity of 96.95% and 96.93% to Flavobacterium nitrogenifigens NXU-44^T and Flavobacterium compostarboris 15C3^T, respectively. Based on phenotypic and phylogenetic distinctiveness, strain I3-3^T is considered as a member of novel species within the genus Flavobacterium, for which Flavobacterium amnigenum sp. nov. is proposed. The type strain is I3-3^T (=KCTC 52884^T =NBRC 112871^T).

Genotypic and phenotypic diversity of Lactobacillus rossiae isolated from beer

AIMS

Over the past few years, the lactic acid bacteria (LAB) species Lactobacillus rossiae has appeared on occasion as a beer spoiler, in addition to its role as an inhabitant of sourdough and other foods. Many authors have described the L. rossiae sourdough isolates as phenotypically and genotypically extremely versatile. This characterization was confirmed in a comprehensive genotypic and phenotypic study based on 11 beer-related L. rossiae isolates.

MATERIALS AND METHODS

The beer-related isolates and the L. rossiae type strain were classified in a polyphasic approach applying 16S rRNA, rpoA and pheS housekeeping gene sequence comparisons, DNA-DNA hybridization and rep-PCR technique. Additionally, carbohydrate fermentation and amino-acid metabolism were examined. In terms of the beer-spoilage ability, the growth in two different beer types was examined and the presence of three prominent hop resistance genes (horA, horC and hitA) and of one gene presumably responsible for the production of exopolysaccharides (gtf) was checked.

CONCLUSION

The carbohydrate fermentation pattern (GTG)₅ rep-PCR and the pheS gene sequence comparison showed deviations between sourdough and beer-related isolates. DNA-DNA hybridization values and the pheS gene sequence comparison between beer-related isolates point towards the need for expansion of the limits for species description.

SIGNIFICANCE AND IMPACT OF THE STUDY

Lactobacillus rossiae shows great phenotypic and genotypic variability stretching the limits of species description. The correlation between pheS gene sequence and the presence of the horC gene is important for brewing microbiologists and the search for beer-spoilage prediction methods.

Glycomyces xiaoerkulensis sp. nov., isolated from Xiaoerkule lake in Xinjiang, China

A novel actinomycete, strain TRM 41368^T, was isolated from a silt sample from Xiaoerkule lake in Xinjiang province, China, and was examined using a polyphasic approach. Strain TRM 41368^T was aerobic, Gram-stain-positive, with an optimum NaCl concentration for growth of 5 % (w/v), and an optimum temperature for growth of 35-37 °C. On the basis of 16S rRNA gene sequence analysis, strain TRM 41368^T was most closely related to Glycomycesfuscus TRM 49117^T (98.46 % similarity). However, it had a relatively low DNA-DNA relatedness value with G. fuscus TRM 49117^T (ANI=70.59 %). The organism had chemical and morphological features typical of the genus Glycomyces. The cell wall of TRM 41368^T contained meso-diaminopimelic acid; xylose, ribose and glucose were the major whole-cell sugars. The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositolmannosides. The predominant menaquinone was MK-9(H6). The major fatty acids were C18 : 1ω9c, C16 : 0, iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The G+C content of the DNA was 69.9 mol%. On the basis of the polyphasic evidence, strain TRM 41368^T should be designated as a novel species of the genus Glycomyces, for which the name Glycomyces xiaoerkulensis sp. nov. is proposed. The type strain is TRM 41368^T (=CCTCC AA 2017005^T=KCTC 39932^T).

Soonwooa purpurea sp. nov., isolated from a fresh water river

A pale-brown-coloured, rod-shaped, non-motile, and Gram-reaction-negative bacterium, strain I54^T, was isolated from a water sample of a freshwater river in Iksan, Republic of Korea. The phylogenetic affiliation based on 16S rRNA gene sequence analysis showed that strain I54^T belonged to the genus Soonwooa of the family Flavobacteriaceae with a sequence similarity of 97.5 % to Soonwooa buanensis HM0024^T. The major fatty acids (>5 %) of strain I54^T were iso-C15 : 0, anteiso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and iso-C17 : 0 3-OH. Phosphatidylethanolamine, one aminolipid and two unknown lipids were the major polar lipids. The G+C content of the genomic DNA was 34.2 (±0.3)mol% and MK6 was the sole respiratory quinone. On the basis of its molecular and phenotypic characteristics, strain I54^T represents a novel species in the genus Soonwooa, for which the name Soonwooapurpurea sp. nov. is proposed. The type strain is I54^T (=KCTC 52722^T=JCM 31880^T).

Tenacibaculum agarivorans sp. nov., an agar-degrading bacterium isolated from marine alga Porphyra yezoensis Ueda

A novel Gram-stain-negative, aerobic, rod-shaped, non-flagellated and agar-digesting marine bacterium, designated as HZ1^T, was isolated from the marine alga Porphyra yezoensis Ueda (AST58-103) collected from the coastal area of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences placed HZ1^T in the genus Tenacibaculum, and it formed a distinct clade in the phylogenetic tree with the type strains of Tenacibaculum amylolyticum and Tenacibaculum skagerrakense, with 97.0 % and 96.7 % 16S rRNA gene sequence similarities, respectively. The DNA G+C content of the isolate was 31.8 mol%. HZ1^T contained MK-6 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C15 : 1G as the major fatty acids. The major polar lipids were phosphatidylethanolamine, four unidentified lipids and five unidentified aminolipids. On the basis of the results of the phylogenetic analysis and phenotypic properties, it is concluded that HZ1^T represents a novel species of the genus Tenacibaculum, for which the name Tenacibaculumagarivorans sp. nov. is proposed. The type strain is HZ1^T (=MCCC 1H00174^T=KCTC 52476^T).