Pseudoflavitalea rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere of tomato, and proposal to reclassify Flavitalea soli as Pseudoflavitalea soli comb. nov

Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes

An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by A. colombiense. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.

Longitalea arenae gen. nov., sp. nov. and Longitalea luteola sp. nov., two new members of the family Chitinophagaceae isolated from desert soil

Two strains designated as SYSU D01084^T and SYSU D00799^T, were isolated from a sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells of both strains were Gram-stain-negative, strictly aerobic, long-rod-shaped, oxidase- and catalase-negative, motile or non-motile. Colonies were circular, translucent, convex, smooth and light-yellow in color on R2A agar. The two isolates were found to grow at 4-50 ºC, at pH 6.0-8.0 and with 0-1.0% (w/v) NaCl. Analysis of their 16S rRNA gene sequences indicated that they belonged to the family Chitinophagaceae, and closely related to the genera Paraflavitalea, Niastella, Pseudoflavitalea and Flavitalea. The two novel strains shared 98.1% 16S rRNA sequence similarity and represent different species on the basis of low average nucleotide identity (ANI, 83.8%) and digital DNA-DNA hybridization (dDDH, 51.4%) values. The genomic DNA G + C contents of strains SYSU D01084^T and SYSU D00799^T were 46.0 and 45.6%, respectively. Phylogenetic trees showed that the two isolates were clustered in an individual lineage and not grouped consistently into any specific genus. The polar lipids contained of phosphatidylethanolamine, four unidentified aminolipids, two unidentified aminoglycolipids, and three or four unidentified lipids. The predominant respiratory quinone was MK-7 and the major fatty acids (> 10%) were identified as iso-C_15:0, iso-C_17:0 3-OH, and iso-C_15:1 G. Based on the combined phenotypic, genomic and phylogenetic analyses, the two strains represent two novel species of a new genus in the family Chitinophagaceae, for which the name Longitalea gen. nov. is proposed, comprising the type species Longitalea arenae sp. nov. (type strain SYSU D01084^T = CGMCC 1.18641^T = MCCC 1K05006^T = KCTC 82283^T) and Longitalea luteola sp. nov. (type strain SYSU D00799^T = MCCC 1K04987^T = KCTC 82282^T = NBRC 114888^T).

Hanamia caeni gen. nov., sp. nov., a Member of the Family Chitinophagaceae Isolated from Activated Sludge in Korea

A novel Gram-stain-negative, aerobic, yellowish-pigmented, non-motile, rod-shaped bacterial strain, designated strain BO-59^T, was isolated from the activated sludge of a wastewater treatment plant in Hanam City, South Korea. Phylogenetic study based on the 16S rRNA gene sequence positioned BO-59^T in a distinct lineage in the family Chitinophagaceae, sharing less than 92.8% sequence similarity with members of the closely related genera Ferruginibacter, Flavitalea, Pseudoflavitalea, Flavisolibacter, Niastella, and Terrimonas. Phylogenomic- and genomic relatedness analyses revealed that strain BO-59^T is clearly distinguished from other genera in the family Chitinophagaceae by average nucleotide identity < 66.9%) and the genome-to-genome distance (< 29.5%) values. The strain BO-59^T contained MK-7 as the predominant quinone, and iso-C_15:0, iso-C_17:0 3OH, and iso-C_15:1 G as major fatty acids (> 10%). The DNA G + C content was 39.1 mol% based on genome sequence analysis. The polar lipids of strain BO-59^T were phosphatidylethanolamine, an unidentified aminophospholipid and three unidentified polar lipids. 16S rRNA gene sequence similarity, physiological, and biochemical characteristics indicated that strain BO-59^T represents a novel species of a new genus, for which the name Hanamia caeni gen. nov., sp. nov. is proposed. The type strain is BO-59^T (= KACC 19646^T = LMG 30865 ^T).

Back to the Future: Decomposability of a Biobased and Biodegradable Plastic in Field Soil Environments and Its Microbiome under Ambient and Future Climates

Decomposition by microorganisms of plastics in soils is almost unexplored despite the fact that the majority of plastics released into the environment end up in soils. Here, we investigate the decomposition process and microbiome of one of the most promising biobased and biodegradable plastics, poly(butylene succinate-co-adipate) (PBSA), under field soil conditions under both ambient and future predicted climates (for the time between 2070 and 2100). We show that the gravimetric and molar mass of PBSA is already largely reduced (28-33%) after 328 days under both climates. We provide novel information on the PBSA microbiome encompassing the three domains of life: Archaea, Bacteria, and Eukarya (fungi). We show that PBSA begins to decompose after the increase in relative abundances of aquatic fungi (Tetracladium spp.) and nitrogen-fixing bacteria. The PBSA microbiome is distinct from that of surrounding soils, suggesting that PBSA serves as a new ecological habitat. We conclude that the microbial decomposition process of PBSA in soil is more complex than previously thought by involving interkingdom relationships, especially between bacteria and fungi.

Paraflavitalea devenefica sp. nov., isolated from urban soil

A Gram-stain-negative, rod-shaped, mesophilic, milky white-pigmented, aerobic, non-spore-forming and non-flagellated bacterium, designated strain X16^T, was isolated from urban soil of Zibo, Shandong, China. According to 16S rRNA gene sequence analysis, the isolate showed highest similarities with Paraflavitalea soli 5GH32-13^T (97.6 %), Pseudoflavitalea soli KIS20-3^T (96.2 %), Pseudobacter ginsenosidimutans Gsoil 221^T (96.0 %) and Pseudoflavitalea rhizosphaerae T16R-265^T (95.8 %). The neighbour-joining tree based on 16S rRNA gene sequences showed that strain X16^T formed a subcluster with Paraflavitalea soli 5GH32-13^T, and the subcluster was closely related to Pseudoflavitalea soli KIS20-3^T, Pseudobacter ginsenosidimutans Gsoil 221^T and Pseudoflavitalea rhizosphaerae T16R-265^T. Strain X16^T also formed a subcluster with Paraflavitalea soli 5GH32-13^T in phylogenetic tree based on genomic sequences. The polar lipids are phosphatidylethanolamine, two unknown aminolipids, two unknown aminophospholipids, two unknown lipids and two unknown phospholipids. The major quinone of strain X16^T is menaquinone-7 and the main fatty acids (>10 % of total fatty acids) of strain X16^T are iso-C_15 : 0, iso-C_17 : 0 3-OH and iso-C_15 : 1 G. The genome length of strain X16^T is 8.7 Mb with a DNA G+C content of 47.4 %. ANI values among strain X16^T and strain Paraflavitalea soli 5GH32-13^T, Pseudobacter ginsenosidimutans Gsoil 221^T, and Pseudoflavitalea rhizosphaerae T16R-265^T are 78.1, 70.7, 70.6 %, respectively. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain X16^T represents a novel species. Besides, strain X16^T can detoxify high toxicity selenite [Se(IV)] to low toxicity elemental selenium [Se(0)], for which the name Paraflavitale devenefica sp. nov. is proposed. The type strain is X16^T (=KACC 21698^T=GDMCC1.1757^T).

Agriterribacter humi gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from soil of a farming field

A Gram-stain-negative bacterium, designated strain YJ03^T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ03^T was found to be an aerobic, non-motile and non-spore-forming bacterium which can grow at 10-33 °C (optimum, 25-28 °C), at pH 6.6-9.5 (optimum, pH 7.0-7.5) and at salinities of 0-1.0 % (w/v) NaCl (optimum, 0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ03^T with the closely related relatives were in the range 93.9-92.2 %, and the results of phylogenomic analysis indicated that strain YJ03^T was clearly separated from species of the genera in the family Chitinophagaceae, showing average nucleotide identity values of 68.8-64.3 %. The predominant isoprenoid quinone was identified as MK-7 and the major fatty acids were iso-C_15 : 0, iso-C_17 : 0 3-OH and an unidentified fatty acid with an equivalent chain-length of 13.565. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and six unidentified lipids. The G+C content of the genome was determined to be 41.8 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences in this study, strain YJ03^T is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Agriterribacter humi gen. nov., sp. nov., is proposed. The type strain of Agriterribacter humi is YJ03^T (=KACC 19548^T=NBRC 113195^T).

Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov

A Gram-stain-negative, microaerophilic, non-motile, rod-shaped bacterium strain designated PMP191F^T, was isolated from a human peritoneal tumour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism formed a lineage within the family Chitinophagaceae that was distinct from members of the genus Pseudoflavitalea (95.1-95.2 % sequence similarity) and Pseudobacter ginsenosidimutans (94.4 % sequence similarity). The average nucleotide identity values between strain PMP191F^T and Pseudoflavitalea rhizosphaerae T16R-265^T and Pseudobacter ginsenosidimutans Gsoil 221^T was 68.9 and 62.3% respectively. The only respiratory quinone of strain PMP191F^T was MK-7 and the major fatty acids were iso-C_15 : 0, iso-C_15 : 1 G and summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine and some unidentified amino and glycolipids. The G+C content of strain PMP191F^T calculated from the genome sequence was 43.4 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strain PMP191F^T represents a novel species and genus for which the name Parapseudoflavitalea muciniphila gen. nov., sp. nov. is proposed. The type strain is PMP191F^T (=DSM 104999^T=ATCC BAA-2857^T = CCUG 72691^T). The phylogenetic analyses also revealed that Pseudobacter ginsenosidimutans shared over 98 % sequence similarly to members of the genus Pseudoflavitalea. However, the average nucleotide identity value between Pseudoflavitalea rhizosphaerae T16R-265^T, the type species of the genus and Pseudobacter ginsenosidimutans Gsoil 221^T was 86.8 %. Therefore, we also propose that Pseudobacter ginsenosidimutans be reclassified as Pseudoflavitalea ginsenosidimutans comb. nov.

Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses

Chronic otitis media with effusion (COME) is a common childhood disease characterized by an accumulation of fluid behind the eardrum. COME often requires surgical intervention and can also lead to significant hearing loss and subsequent learning disabilities. Recent characterization of the middle ear fluid (MEF) microbiome in pediatric patients has led to an improved understanding of the microbiota present in the middle ear during COME. However, it is not currently known how the MEF microbiome might vary due to other conditions, particularly respiratory disorders. Here, we apply an amplicon sequence variant (ASV) pipeline to MEF 16S rRNA high-throughput sequencing data from 50 children with COME (ages 3–176 months) undergoing tube placement. We achieve a more detailed taxonomic resolution than previously reported, including species and genus level resolution. Additionally, we provide the first report of the functional roles of the MEF microbiome and demonstrate that despite high taxonomic diversity, the functional capacity of the MEF microbiome remains uniform between patients. Furthermore, we analyze microbiome differences between children with COME with and without a history of lower airway disease (i.e., asthma or bronchiolitis). The MEF microbiome was less diverse in participants with lower airway disease than in patients without, and phylogenetic β-diversity (weighted UniFrac) was significantly different based on lower airway disease status. Differential abundance between patients with lower airway disease and those without was observed for the genera Haemophilus, Moraxella, Staphylococcus, Alloiococcus, and Turicella. These findings support previous suggestions of a link between COME and respiratory illnesses and emphasize the need for future study of the middle ear and respiratory tract microbiomes in diseases such as asthma and bronchiolitis.

Gynurincola endophyticus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae

A Gram-stain-negative, rod-shaped (0.2-0.4 µm×1.2-1.7 µm), endophytic bacterium, designated HBUM179779^T, was isolated from the stem of a medicinal plant,Gynura bicolor, collected from Pixian county in Sichuan province, China. The strain did not produce endospores and its cells could secrete mucus. The predominant menaquinone was MK-7. The polar lipids were phosphatidylethanolamine, phosphatidylinositolmannosides, two unknown aminolipids, two unknown glycolipids and an unknown phospholipid. Branched fatty acids (iso-) and hydroxy fatty acids were the main fatty acids, which mainly included iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HBUM179779^T fell within the family Chitinophagaceae, and its closest neighbour was Pseudoflavitalea rhizosphaerae T16R-265^T (94.46 %). However, strain HBUM179779^T did not make a coherent clade with members of the recognized organisms. The average nucleotide identity value between strain HBUM179779^T and Pseudoflavitalea rhizosphaerae T16R-265^T was 67.1 %. On the basis of the phylogenetic and phenotypic characteristics of this bacterium, a novel genus and species, Gynurincola endophyticus gen. nov., sp. nov., is proposed. The type strain is HBUM179779^T (=CGMCC 1.15525^T=NBRC 112424^T).

Flavitalea flava sp. nov., a bacterium isolated from a soil sample, and emended description of the genus Flavitalea

A Gram-stain negative strain, designated AN120636^T, was isolated from a soil sample collected from Goesan-gun, Chungbuk, South Korea. The strain was strictly aerobic, with golden yellow-pigmented colonies on R2A agar. Cells were non-motile, long or short rods and some were observed to be coccal. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain AN120636^T belongs to the genus Flavitalea in the family of Chitinophagacea, with Flavitalea populi (95.4%), Pseudoflavitalea soli (95.0%), Flavitalea gansuensis (94.7%) and Pseudoflavitalea rhizosphaerae (94.7%) as its close relatives. Growth was observed at 15-32 °C, pH 5.0-7.0 and in the absence of NaCl. The strain contained iso-C_17:0 3-OH, iso-C_15:1 G and iso-C_15:0 as its major cellular fatty acids; phosphatidylethanolamine as the major polar lipid; MK-7 as its respiratory quinone; and the polyamine was homospermidine. The genomic DNA G+C content was 44.8 mol%. On the basis of the polyphasic evidence, strain AN120636^T is considered to represent a novel species, for which the name Flavitalea flava sp. nov. is proposed. The type strain is AN120636^T (=KCTC 52346^T=CCTCC AB 2017174^T).

Niveitalea solisilvae gen. nov., sp. nov., isolated from forest soil and emended description of the genus Flavihumibacter Zhang et al. 2010

A Gram-stain-negative and strictly aerobic bacterial strain, designated 6-4T, was isolated from forest soil in Jeju island, South Korea. Cells showing oxidase-positive and catalase-negative reactions were thin and long non-motile rods. Growth of strain 6-4T was observed at 20-35 °C (optimum, 30 °C) and pH 6.0-9.0 (optimum, pH 7.0). Strain 6-4T contained iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH as the major fatty acids and menaquinone-7 (MK-7) as the sole isoprenoid quinone. Phosphatidylethanolamine was the major polar lipid and five unidentified aminolipids, one unidentified aminophospholipid and one unidentified lipid were also detected as minor polar lipids. The G+C content of the genomic DNA was 45.8 mol%. Strain 6-4T was most closely related to Flavihumibacter solisilvae 3-3T with a low 16S rRNA gene sequence similarity (94.2 %) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from members of the genus Flavihumibacter and other closely related genera. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain 6-4T represents a novel species of a new genus of the family Chitinophagaceae, for which the name Niveitalea solisilvae gen. nov., sp. nov. is proposed. The type strain of Niveitalea solisilvae is 6-4T (=KACC 18808T=JCM 31525T). An emended description of the genus Flavihumibacter is also proposed.