Comparative genome analysis of the genus Hydrotalea and proposal of the novel species Hydrotalea lipotrueae sp. nov., isolated from a groundwater aquifer in the south of Mallorca Island, Spain

From a collection of > 140 strains isolated from groundwater with thermal anomalies for the purpose of obtaining good candidates with applications in the cosmetic industry, two strains were selected because of their taxonomic novelty. Among the isolates, strains TMF_100^T and TFM_099 stood out for their potential biotechnological relevance, and a comparative analysis of 16S rRNA gene sequences indicated that these strains represented a new species of the genus Hydrotalea. In addition, from the public genomic databases, metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) could be retrieved that affiliated with this genus. These MAGs and SAGs had been obtained from different environmental samples, such as acid mine drainage or marine sediments. In addition to the description of the new species, the ecological relevance of the members of this genus was demonstrated by means of denitrification, CRISPR-Cas system diversity and heavy metal resistance, as well as their wide geographical distribution and environmental versatility. Supported by the taxonomic study, together with physiological and morphological differences and ecological features, we concluded that strain TMF_100^T represented a novel species within the genus Hydrotalea, for which we propose the name Hydrotalea lipotrueae sp. nov.

Limnovirga soli gen. nov., sp. nov., isolated from river sediment

A cream-coloured, Gram-stain-negative, rod-shaped bacterium, designated strain KSC-6^T, was isolated from soil sampled at the Gapcheon River watershed in Daejeon, Republic of Korea. The organism does not require NaCl for growth and grows at pH 6.0-8.0 (optimum, pH 7.0) and 10-37 °C (optimum, 25 °C). Phylogenetic trees based on the 16S rRNA gene sequences reveal that strain KSC-6^T belongs to the family Chitinophagaceae within the order Chitinophagales and is most closely related to Panacibacter ginsenosidivorans Gsoil 1550^T (95.9% similarity). The genomic DNA G+C content was 38.9 mol%. The major cellular fatty acids (>8 %) of strain KCS-6^T were iso-C_15:0, iso-C_15 : 1 G and iso-C_17 : 0 3-OH. The predominant respiratory quinone was menaquinone 7 and the predominant polar lipids were phosphatidylethanolamine, five unidentified aminolipids and two unidentified lipids. Based on genome analyses, low digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values with closely related genera, and differential chemotaxonomic and physiological properties, we suggest that strain KCS-6^T represents a novel species in a new genus in the family Chitinophagaceae, for which the name Limnovirga soli gen. nov., sp. nov. (type strain KCS-6^T=KCCM 43337^T=NBRC 114336^T) is proposed.

Urban Aerobiomes are Influenced by Season, Vegetation, and Individual Site Characteristics

Exposure to biodiverse environments such as forests can benefit human well-being, and evidence suggests exposure to high microbial diversity may improve mental and immune health. However, the factors that drive microbial community assembly are poorly understood, as is the relationship between exposure to these communities and human health. We characterized airborne bacterial communities in two disparate types of urban greenspace (forest and grass) in late-spring 2017 at sites previously sampled in late-summer 2015 in Eugene-Springfield, Oregon, using high-throughput metabarcode sequencing. While all sites shared a core aerobiome in late-spring consisting of plant- and soil-associated genera, forests had significantly higher diversity than grass sites (F = 12, P = 0.004). Vegetation type explained 14% of the difference between forest and grass aerobiomes, yet individual site location explained 41% of the variation. These results were similar to but amplified over those from late summer, suggesting that both aerobiome diversity and vegetation-driven effects are higher when deciduous foliage is fresher and more active, temperatures cooler, and humidity higher. Continued exploration and hypothesis-driven research will enable development of mechanistic theory describing key drivers of urban aerobiome assembly and its relationship to human health, which, in turn, will help urban designers and planners create evidence-based salutogenic cities for future generations.

Detection of the deep biosphere in metamorphic rocks from the Chinese continental scientific drilling

It is generally accepted that there is a vast, well-populated biosphere in the subsurface, but the depth limit of the terrestrial biosphere has yet to be determined, largely because of the lack of access to the subsurface. Here as part of the Chinese Continental Scientific Drilling (CCSD) project in eastern China, we acquired continuous rock cores and endeavored to probe the depth limit of the biosphere and the depth-dependent distribution of microorganisms at a geologically unique site, that is, a convergent plate boundary. Microbiological analyses of ultra-high-pressure metamorphic rock cores taken from the ground surface to 5,158-meter reveal that microbial distribution was continuous up to a depth of ~4,850 m, where temperature was estimated to be ~137°C. The metabolic state of these organisms at such great depth remains to be determined. Microbial abundance, ranging from 10³ to 10⁸  cells/g, was also related to porosity, but not to the depth and rock composition. In addition, microbial diversity systematically decreased with depth. Our results support the notion that temperature is a key factor in determining the lower limit of the biosphere in the continental subsurface.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria

Gaiella occulta strain F2‐233^T (=CECT 7815 = LMG 26412), isolated from a 150 meter deep mineral water aquifer, was deemed a candidate for high‐quality draft genome sequencing because of the rare environment from which it was isolated. The draft genome sequence (QQZY00000000) of strain F2‐233^T is composed of approximately 3 Mb, predicted 3,119 protein‐coding genes of which 2,545 were assigned putative functions. Genome analysis was done by comparison with the other deep‐branching Actinobacteria neighbors Rubrobacter radiotolerans, Solirubrobacter soli and Thermoleophilum album. The genes for the tricarboxylic acid cycle, gluconeogenesis and pentose phosphate pathway, were identified in G. occulta, R. radiotolerans, S. soli and T. album genomes. Genes of the Embden–Meyerhof–Parnas pathway and nitrate reduction were identified in G. occulta, R. radiotolerans and S. soli, but not in the T. album genome. Alkane degradation is precluded by genome analysis in G. occulta. Genes involved in myo‐inositol metabolism were found in both S. soli and G. occulta genomes. A Calvin–Benson–Bassham (CBB) cycle with a type I RuBisCO was identified in G. occulta genome, as well. However, experimental growth under several conditions was negative and CO₂ fixation could not be proven in G. occulta.

Edaphobaculum flavum gen. nov., sp. nov., a member of family Chitinophagaceae, isolated from grassland soil

A yellow-coloured, Gram-stain-negative, non-motile, rod-shaped, strictly aerobic bacterium, designated 1-116^T, was isolated from Erdos grassland soil of Inner Mongolia, PR China. Phylogenetic analysis based on 16S rRNA genes showed that strain 1-116^T was a member of family Chitinophagaceae and exhibited the highest similarities to Taibaiella koreensis THG-DT86^T (90.1 %) and Flavihumibacter solisivae 3-3^T (90.0 %), while the similarities to the other Chitinophagaceae type strains were lower than 90.0 %. Strain 1-116^T grew at 16-33 °C (optimum 28 °C), pH 6.0-9.0 (optimum 7.0-8.0) and 0-0.5 % NaCl (w/v; optimum without NaCl). A flexirubin-type pigment was present. The DNA G+C content was 43.2 mol% and the only quinone present was menaquinone-7. The only polyamine detected was sym-homospermidine [30.7 µmol (g dry weight)^-1] and the predominant fatty acids were iso-C15 : 0 (20.8 %), iso-C15 : 1 G (25.1 %), summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I; 13.8 %) and iso-C17 : 0 3-OH (13.2 %). The major polar lipids were phosphatidylethanolamine, three unidentified lipids, an unidentified aminophospholipid and an unidentified glycolipid. On the basis of the polyphasic analyses, strain 1-116^T represents a novel genus and species in the family Chitinophagaceae, for which the name Edaphobaculum flavum gen. nov., sp. nov., is proposed. The type strain of Edaphobaculum flavum is 1-116^T (=CCTCC AB 2017054=KCTC 52843).

Whole-Genome Sequence of Filimonas lacunae, a Bacterium of the Family Chitinophagaceae Characterized by Marked Colony Growth under a High-CO2 Atmosphere

We report here the genome sequence of Filimonas lacunae, a bacterium of the family Chitinophagaceae characterized by high-CO2-dependent growth. The 7.81-Mb circular genome harbors many genes involved in carbohydrate degradation and related genetic regulation, suggesting the role of the bacterium as a carbohydrate degrader in diverse environments.

Compostibacter hankyongensis gen. nov.,  sp. nov., isolated from compost

A novel bacterial strain, designated strain BS27T, was isolated from mushroom compost and subjected to a taxonomic study using a polyphasic approach. Colonies of BS27T were milky-white, circular with regular fringes and opaque. Cells were short rods, 0.3-0.5 µm wide and 1.2-2.0 µm long. Phylogenetic study based on the 16S rRNA gene sequence placed BS27T in a distinct lineage in the family Chitinophagaceae, sharing 90.1-90.9 % sequence similarity with members of the closely related genera Chitinophaga, Flavitalea, Flavihumibacter, Lacibacter and Flavisolibacter. The novel isolate showed the highest sequence similarities with the members of the genus Chitinophaga. BS27T contained MK-7 as predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and iso-C17 : 1I and/or anteiso-C17 : 1B (summed feature 4) as major fatty acids. The DNA G+C content was 53.0 mol%. The major polar lipids of BS27T were phosphatidylethanolamine (PE) and five unidentified polar lipids (L1, L2, L5, L6 and L7). The results of physiological and biochemical tests allowed phenotypic differentiation of BS27T from its closest phylogenetic neighbours. On the basis of the evidence of this polyphasic study, isolate BS27T represents a novel genus and species in the family Chitinophagaceae for which the name Compostibacter hankyongensisgen. nov., sp. nov. is proposed. The type strain is BS27T (=KACC 18745T=JCM 17664T).

Filimonas zeae sp. nov., an endophytic bacterium isolated from maize root

A novel Gram-stain-negative, aerobic, motile by gliding and filamentous strain, designated 772^T,was isolated from surface-sterilized root tissue of maize planted in the Fangshan District of Beijing, China. 16S rRNA gene sequence analysis indicated that strain 772^T was closely related to Filimonas endophytica SR2-06^T andFilimonas lacunae YT21^T of the family Chitinophagaceae with sequence similarities of 99.0 and 96.9 %, respectively. However, the new isolate exhibited relatively low levels of DNA-DNA relatedness with respect to Filimonas. endophytica KCTC 42060^T (18.7±1.8 %) and Filimonas. lacunae DSM 21054^T (17.9±2.0%). The DNA G+C content of strain 772^T was 44.9 mol%. The respiratory quinone was menaquinone-7 and the polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and one unidentified lipid. The major fatty acids were iso-C15 : 0 and iso-C15 : 1 G. The results of the physiological and biochemical tests and minor differences in the fatty acid profiles allowed the clear phenotypic differentiation of strain 772^T from the closely related species Filimonas. endophytica andF. lacunae. Strain 772^T thus represents a novel species within the genus Filimonas, for which the name Filimonas zeae sp. nov. is proposed. The type strain is 772^T (=CGMCC 1.15290^T=DSM 100760^T).

Hydrobacter penzbergensis gen. nov., sp. nov., isolated from purified water

A Gram-negative, oxidase- and catalase-positive bacterium, designated strain EM 4(T), which varied in shape from rod-shaped to curved or helical with frequently observed bulb-shaped protuberances, was isolated from purified water. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the family Chitinophagaceae within the phylum Bacteroidetes; the closest relative among bacterial species with validly published names was determined to be Sediminibacterium salmoneum NBRC 103935(T), with 93.4 % sequence identity. The main fatty acids of strain EM 4(T) were iso-C15 : 0, iso-C15 : 1 and iso-C17 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, aminolipids, aminophospholipids and unknown lipids; the quinone system consisted of menaquinone MK-7. 16S rRNA gene sequence analysis and the polar lipid and fatty acid profiles suggest that the strain represents a novel genus and species, for which the name Hydrobacter penzbergensis gen. nov., sp. nov. is proposed. The type strain of Hydrobacter penzbergensis is strain EM 4(T) ( = DSM 25353(T) = CCUG 62278(T)).

Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil

A Gram-stain-negative, short rod-shaped, non-flagellated, yellow bacterium, designated strain 5GHs7-2T, was isolated from a greenhouse soil sample in South Korea. 16S rRNA gene sequence analysis of strain 5GHs7-2T indicated that the isolate belonged to the family Chitinophagaceae , and exhibited the highest sequence similarities with members of the genera Terrimonas (89.2–92.6 %), Sediminibacterium (90.8–91.4 %) and Chitinophaga (89.2–91.7 %), Filimonas lacunae YT21T (91.7 %), members of the genus Segetibacter (90.2–91.6 %), Parasegetibacter luojiensis RHYL-37T (90.9 %) and Flavihumibacter petaseus T41T (91.2 %). Flexirubin-type pigments were present. The major cellular fatty acids of the novel strain were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The polar lipid profile consisted of a large amount of phosphatidylethanolamine, and moderate and small amounts of several unknown aminolipids and lipids. The only respiratory quinone of strain 5GHs7-2T was MK-7, and the DNA G+C content was 47.6 mol%. On the basis of the evidence presented, it is concluded that strain 5GHs7-2T represents a novel species of a new genus in the family Chitinophagaceae , for which the name Parafilimonas terrae gen. nov., sp. nov. is proposed. The type strain of the type species is 5GHs7-2T ( = KACC 17343T = DSM 28286T).

Crenotalea thermophila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a hot spring

A thermophilic aerobic bacterium designated strain STH-1-Y1(T) was isolated from sulfur-turf in a Japanese hot spring (Okuhodaka hot spring, Gifu Pref.). Colonies of strain STH-1-Y1(T) were yellow and low convex morphology with a slightly irregular fringe. Cells were slender long rods, 0.4-0.6 µm wide and 1.2-3.0 µm long. The isolate was an obligate aerophilic organism, and could not grow by fermentation or nitrate respiration. The isolate had a thermophilic trait, and could grow at 35-60 °C and pH 5.5-7.5; maximum growth occurred at 55 °C and pH 7.0 with a doubling time of 1.9 h. The Biolog and API tests suggested that strain STH-1-Y1(T) was able to use various sugars such as glucose, lactose, mannose, maltose, trehalose, cellobiose and sucrose, but could not use sugar alcohols other than glycerol, i.e. adonitol, arabitol, erythritol, inositol, mannitol, sorbitol and xylitol. Lactate and glutamate could be used, but other fatty acids, i.e. acetate, citrate, propionate and succinate could not. Gelatin, casein, starch and glycogen were hydrolysed, but neither chitin nor agar was degraded. Cells lacked flexirubin and showed oxidase and catalase activities. The major respiratory quinone was menaquinone-7 (MK-7), and major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 0 and anteiso-C15 : 0. No unsaturated fatty acids were detected. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain STH-1-Y1(T) was closely related to the family Chitinophagaceae within the phylum Bacteroidetes. However, the isolate was evenly distant from all members in this family with sequence similarities of 87-89 %. These significantly low sequence similarities strongly suggested that strain STH-1-Y1(T) represents a novel species in a new genus of the family Chitinophagaceae within the phylum Bacteroidetes. Based on phenotypic and phylogenetic characteristics, the name Crenotalea thermophila gen. nov., sp. nov. is proposed. The type strain of the type species is STH-1-Y1(T) ( = JCM 11541(T) = DSM 14807(T)).