Leucobacter edaphi sp. nov., a highly chromate-tolerant bacterium isolated from chromium containing chemical plant soil

A Gram-positive, aerobic, rod-shaped non-motile, non-sporulating bacterium, designated CSA2T, was isolated from chromium-containing soils collected from a chemical plant. The 16S rRNA gene sequence of strain CSA2T showed the highest homology with Leucobacter chromiireducens subsp. solipictus (97.85%), Leucobacter chromiireducens subsp. chromiireducens (97.85%). The digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and the amino acid identity (AAI) values among strains CSA2T and the selected Leucobacter species were 20.6-23.4% (dDDH), 72.67-78.03% (ANI) and 66.39-76.16% (AAI), falling below the recommended thresholds for species delimitation. The principal fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The major menaquinones detected were MK-10 and MK-11. The cell-wall amino acids included 2,4-diaminobutyric acid, threonine, glutamic acid, alanine and glycine. Based on molecular feature, phenotypic and chemotaxonomic, strain CSA2T was considered to be a novel species of the genus Leucobacter., and the name Leucobacter edaphi sp. nov. is proposed. The type strain is CSA2T (= JCM 34360T = CGMCC 1.18747T).

Leucobacter tenebrionis sp. nov., isolated from the gut of Tenebrio molitor

A novel Gram-stain-positive bacterium, designated NB10T, was isolated from the gut of Tenebrio molitor. The isolate was rod-shaped, aerobic, non-motile and non-spore-forming. Colonies of strain NB10T were light yellow, circular and smooth. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that the isolate was related to the genus Leucobacter. Its closest relatives were Leucobacter holotrichiae T14T (97.8 % 16S rRNA gene sequence similarity), Leucobacter zeae CC-MF41T (97.0%) and Leucobacter salsicius M1-8T (96.4%). The DNA G+C content of strain NB10T was 68.8 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization values among strain NB10T and the selected Leucobacter species were ≤83.8 % (ANI-blast), 87.6 % (ANI-MUMmer) and 29.6%, which were below the recommended cutoff values for species delineation. The predominant cellular fatty acids were anteiso-C15 : 0 (39.0%), anteiso-C17 : 0 (35.5%) and iso-C16 : 0 (17.0%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The predominant respiratory quinones were MK-11 and MK-10. The cell wall amino acids were Gly, Glu, Tr, Ala, and DAB. Based on these phylogenetic and phenotypic results, strain NB10T can be clearly distinguished from all of the recognized species of the genus Leucobacter and is considered to represent a novel species of that genus. The name Leucobacter tenebrionis sp. nov. is proposed, with the type strain NB10T (=MCCC 1K07072T=KCTC 49728T).

Leucobacter chinensis sp. nov., with plant growth-promoting potential isolated from field soil after seven-years continuous maize cropping

A novel Gram-stain-positive, aerobic, non-motile and rod-shaped bacterium, designated strain NC76-1^T, was isolated from soil from a field that had undergone seven years continuous maize cropping from Liuba town located in Zhangye city, Gansu province, PR China. Colonies of strain NC76-1^T were white, opaque and circular with a convex shape. The isolate was found to be able to grow at 10-40 °C (optimum 30 °C), pH 6.0 to 12.0 (optimum 7.0-8.0) and with 0-5.0 % (w/v) NaCl (optimum 0%). On the basis of the results of 16S rRNA gene sequence analysis, the strain fell within the clade of the genus Leucobacter, showing the highest sequence similarities with Leucobacter iarius 40^T (97.4%), Leucobacter aridicollis CIP 108388^T (97.0%), Leucobacter chromiireducens subsp. solipictus TAN 31504^T (96.7%) and Leucobacter denitrificans M1T8B10^T (96.7%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between NC76-1^T and its closest relatives, L. iarius 40^T, L. aridicollis CIP 108388^T, L. chromiireducens subsp. solipictus TAN 31504^T and L. denitrificans M1T8B10^T were ≤73.5 % and 20.3%, respectively. The genomic DNA G+C content of NC76-1^T was 61.5 mol%. It presented MK-11 as the predominant menaquinone. The major cellular fatty acids were anteiso-C_15 : 0 (49.2 %) and iso-C_16 : 0 (35.7%). The major polar lipids were found to be diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminoglycolipid, five glycolipid and one unidentified lipids. The cell wall amino acids were 2,4-diaminobutyric acid, alanine, glutamic acid, glycine and threonine. On the basis of the phylogenetic, phenotypic and chemotaxonomic characteristics, strain NC76-1^T is concluded to represent a novel species within the genus Leucobacter, for which the name Leucobacter chinensis sp. nov. is proposed. The type strain is NC76-1^T (GDMCC 1.2286^T= JCM 34651^T).

Microbial community origin and fate through a rural wastewater treatment plant

Conventional wastewater treatment relies on a complex microbiota; however, much of this community is still to be characterised. To better understand the origin, dynamics and fate of bacteria within a wastewater treatment plant: untreated primary wastewater, activated sludge, and post-treatment effluent were characterised. From 3,163 Exact Sequence Variants (ESVs), 860 were annotated to species-level. In primary wastewater, 28% of ESVs were putative bacterial species previously associated with humans, 14% with animals and 5% as common to the environment. Differential abundance analysis revealed significant relative reductions in ESVs from potentially humans-associated species from primary wastewater to activated sludge, and significant increases in ESVs from species associated with nutrient cycling. Between primary wastewater and effluent, 51% of ESVs from human-associated species did not significantly differ, and species such as Bacteroides massiliensis and Bacteroides dorei increased. These findings illustrate that activated sludge increased extracellular protease and urease-producing species, ammonia and nitrite oxidizers, denitrifiers and specific phosphorus accumulators. Although many human-associated species declined, some persisted in effluent, including strains of potential health or environmental concern. Species-level microbial assessment may be useful for understanding variation in wastewater treatment efficiency as well as for monitoring the release of microbes into surface water and the wider ecosystem. This article is protected by copyright. All rights reserved.

Leucobacter soli sp. nov., from soil amended with humic acid

A Gram-positive, non-spore-forming actinobacterium (IMT-300^T) was isolated from soil amended with humic acid in Malvern, AL, USA. This soil has been used for 50+years for the cultivation of earthworms for use as fish bait. Based on 16S rRNA gene sequence similarity studies, strain IMT-300^T was shown to belong to the genus Leucobacter and was closely related to the type strain of 'Leucobacter margaritiformis' L1^T (97.8%). Similarity to all other type strains of Leucobacter species was lower than 97.2 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the IMT-300^T genome assembly and those of the closest relative Leucobacter type strain were 81.4 and 23.3 % (Leucobacter chironomi), respectively. The peptidoglycan of strain IMT-300^T contained l-2,4-diaminobutyric acid as the diagnostic diamino acid. In addition, glycine, d- and l-alanine and d-glutamic acid were found. The peptidoglycan type represents a variant of B2δ (B11). The major quinones were menaquinones MK-10 and MK-11. The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol and moderate to minor amounts of two unidentified phospholipids, two unidentified glycolipids and an unidentified aminophospholipid. The polyamine pattern contained major amounts of spermidine and spermine. Strain IMT-300^T contained the major fatty acids C_15 : 0 anteiso, C_16 : 0 iso and C_17 : 0 anteiso, like other members of the genus Leucobacter. The results of ANI and dDDH analyses and physiological and biochemical tests allowed a genotypic and phenotypic differentiation of strain IMT-300^T from the most closely related Leucobacter species. Strain IMT-300^T represents a novel Leucobacter species, for which we propose the name Leucobacter soli sp. nov., with the type strain IMT-300^T (CIP 111803^T=DSM 110505^T=CCM 9020^T=LMG 31600^T).

Leucobacter coleopterorum sp. nov., Leucobacter insecticola sp. nov., and Leucobacter viscericola sp. nov., isolated from the intestine of the diving beetles, Cybister brevis and Cybister lewisianus, and emended description of the genus Leucobacter

Three novel bacterial strains, HDW9A^T, HDW9B^T, and HDW9C^T, isolated from the intestine of the diving beetles Cybister lewisianus and Cybister brevis, were characterized as three novel species using a polyphasic approach. The isolates were Gram-staining-positive, strictly aerobic, non-motile, and rod-shaped. They grew optimally at 30°C (pH 7) in the presence of 0.5% (wt/vol) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that they belong to the genus Leucobacter and are closely related to L. denitrificans M1T8B10^T (98.4-98.7% sequence similarity). Average nucleotide identity (ANI) values among the isolates were 76.4-84.1%. ANI values for the isolates and the closest taxonomic species, L. denitrificans KACC 14055^T, were 72.3-73.1%. The isolates showed ANI values of < 76.5% with all analyzable Leucobacter strains in the EzBioCloud database. The genomic DNA G + C content of the isolates was 60.3-62.5%. The polar lipid components were phosphatidylglycerol, diphosphatidylglycerol, and other unidentified glycolipids, phospholipids, and lipids. The major cellular fatty acids were anteiso-C_15:0, iso-C_16:0, and anteiso-C_17:0. MK-10 was the major respiratory quinone, and MK-7 and MK-11 were the minor respiratory quinones. The whole-cell sugar components of the isolates were ribose, glucose, galactose, and mannose. The isolates harbored L-2,4-diaminobutyric acid, L-serine, L-lysine, L-aspartic acid, glycine, and D-glutamic acid within the cell wall peptidoglycan. Based on phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses, strains HDW9A^T, HDW9B^T, and HDW9C^T represent three novel species within the genus Leucobacter. We propose the name Leucobacter coleopterorum sp. nov. for strain HDW9A^T (= KACC 21331^T = KCTC 49317^T = JCM 33667^T), the name Leucobacter insecticola sp. nov. for strain HDW9B^T (= KACC 21332^T = KCTC 49318^T = JCM 33668^T), and the name Leucobacter viscericola sp. nov. for strain HDW9C^T (= KACC 21333^T = KCTC 49319^T = JCM 33669^T).

Lacisediminihabitans profunda gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from freshwater sediment

A novel Gram-stain-positive bacterial strain, CHu50b-6-2^T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of strain CHu50b-6-2^T were aerobic non-motile and formed yellow colonies on R2A agar. The phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the family Microbacteriaceae, exhibiting 98.0%, 97.7% and 97.6% 16S rRNA gene sequence similarities to Glaciihabitans tibetensis KCTC 29148^T, Frigoribacterium faeni KACC 20509^T and Lysinibacter cavernae DSM 27960^T, respectively. The phylogenetic trees revealed that strain CHu50b-6-2^T did not show a clear affiliation to any genus within the family Microbacteriaceae. The chemotaxonomic results showed B1α type peptidoglacan containg 2, 4-diaminobutyric acid (DAB) as the diagnostic diamino acid, MK-10 as the predominant respiratory menaquinone, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified glycolipid as the major polar lipids, anteiso-C_15:0, iso-C_16:0, and anteiso-C_17:0 as the major fatty acids, and a DNA G + C content of 67.3 mol%. The combined genotypic and phenotypic data showed that strain CHu50b-6-2^T could be distinguished from all genera within the family Microbacteriaceae and represents a novel genus, Lacisediminihabitans gen. nov., with the name Lacisediminihabitans profunda sp. nov., in the family Microbacteriaceae. The type strain is CHu50b-6-2^T (= KCTC 49081^T = JCM 32673^T).

Genome sequence of "Leucobacter massiliensis" sp. nov. isolated from human pharynx after travel to the 2014 Hajj

"Leucobacter massiliensis" strain 122RC15T sp. nov. is a new species within the genus Leucobacter. The genome of this strain is described here. It was isolated from the pharynx of a 76-year-old Algerian female after travelling from the 2014 Hajj. "Leucobacter massiliensis" is a Gram-positive, aerobic bacillus. Here we describe the features including complete genome and annotation of this strain. The 3 136 406-bp long genome contains 2797 protein-coding genes and 49 RNA genes.

Castellaniella fermenti sp. nov., isolated from a fermented meal

A polyphasic taxonomic approach was used to characterize a presumably novel bacterium, designated strain CC-YTH191^T, isolated from a fermented meal in Taiwan. Cells of strain CC-YTH191^T were Gram-stain-negative aerobic rods, which grew at 15-40 °C (optimal 25-30 °C), pH 6.0-9.0 (optimal 7.0) and 1-2 % (w/v) NaCl (optimal 1 %). On the basis of 16S rRNA gene sequence analysis, strain CC-YTH191^T appeared to belong to the genus Castellaniella, and was closely related to Castellaniella hirudinis (96.7 % similarity), Castellaniella ginsengisoli (96.7 %) and Castellaniella caeni (96.0 %), while with other related species it shared <96.0 % similarity. The major cellular fatty acids of the isolate were C16 : 0, C17 : 0cyclo, C14 : 0 3OH/C16 : 1iso I and C18 : 1ω7c/C18 : 1ω6c. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, three unidentified phospholipids, an unidentified aminolipid and an unidentified aminophospholpid. Putrescine was the predominant polyamine followed by spermidine. The DNA G+C content was 62.2 mol% and the predominant quinone system was ubiquinone 8 (Q-8). All these features confirmed the placement of the strain CC-YTH191^T as a novel species within the genus Castellaniella, for which the name Castellaniella fermenti sp. nov. is proposed. The type strain is CC-YTH191^T (=BCRC 81023^T=JCM 31755^T).

Leucobacter weissii sp. nov., an isolate from activated sludge once described as first representative of the peptidoglycan variation B2δ, and emended description of the genus Leucobacter

Strain S27^T is a Gram-stain-positive, regular rod-shaped, non-motile, non-spore-forming, yellow pigmented actinobacterium which was isolated from an aerated laboratory scale fermenter fed with wastes of a yeast factory. The strain was classified as Microbacterium sp. after the analysis of its peptidoglycan revealed a novel B-type structure established as variation B2δ by Hensel in 1984. As the combination of the peptidoglycan amino acids 2,4-diaminobutyric acid (Dab), threonine (Thr), glycine (Gly), alanine (Ala) and glutamic acid (Glu) is in disagreement with the current genus definition of Microbacterium but is typical of several Leucobacter species, the taxonomic status of strain S27^T was re-examined by a polyphasic study. Comparative analyses of 16S rRNA gene sequences and the occurrence of l-Dab, d-Ala, l-Ala, Gly, l-Thr, d-Glu and lower amounts of l-Glu in the peptidoglycan in combination with the predominating menaquinones MK-11, MK-10 and MK-9, phosphatidylglycerol, and one unknown glycolipid as the major polar lipids (and trace amounts of diphosphatidylglycerol and an unknown phospholipid), a profile with anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C17 : 0 as major fatty acids and the G+C value of 70.1 mol% confirmed the affiliation to the genus Leucobacter and revealed that S27^T (=DSM 20621^T =CCM 8762^T) is the type strain of a new species for which the name Leucobacter weissii sp. nov. is proposed. The availability of new data allows for an emended description of the genus Leucobacter.

Ammoniphilus resinae sp. nov., an endospore-forming bacterium isolated from resin fragments

A polyphasic approach was used to characterize an endospore-forming bacterium, designated strain CC-RT-ET, isolated from resin fragments. Strain CC-RT-ET was Gram-stain-variable and facultatively anaerobic, able to grow at 20-37 °C (optimal 30 °C) and pH6.0-9.0 (optimal pH 7.0). Ellipsoidal and terminal endospores were observed. The 16S rRNA gene sequence analysis of strain CC-RT-ET showed highest sequence similarity to Ammoniphilus oxalivorans RAOx-FST (97.8 %) and Ammoniphilus oxalaticus RAOx-1T (97.7 %). According to the DNA-DNA hybridization, the relatedness values of strain CC-RT-ET with Ammoniphilus oxalivorans RAOx-FST and Ammoniphilus oxalaticus RAOx-1T were 21 % and 29 %, respectively. The DNA G+C content was 39.2 mol% and the predominant quinone system was menaquinone-7 (MK-7). The major polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmethylethanolamine. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The polyamine pattern showed predominance of sym-homospermidine and putrescine. The major fatty acids found in strain CC-RT-ET were C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and C16 : 1ω7c/C16 : 1ω6c. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-RT-ET is considered to represent a novel species of the genus Ammoniphilus, for which the name Ammoniphilus resinaesp. nov. is proposed. The type strain is CC-RT-ET (=BCRC 80314T=DSM 24738T).