Description of Massilia orientalis sp. nov., Isolated from Rhizosphere Soil of Ageratina adenophora

A novel bacteria strain, designated YIM B02787T, was isolated from rhizosphere soil of Ageratina adenophora, in Yunnan, southwest China. The strain was aerobic, Gram-stain-negative, rod-shaped and motile with one polar flagellum. Growth occurred at 4-45 °C (optimum, 20-30 °C) and pH 6.0-10.0 (optimum, 7.0-8.0), and in presence of 0-1% (w/v) NaCl. Phylogenetic analyses based on both 16S rRNA gene and genome sequences data revealed that strain YIM B02787T belongs to the genus Massilia, being closely related to Massilia phosphatilytica KCTC 52513T (98.93% similarity), M. putida KCTC 42761T (98.86%), and M. kyonggiensis JCM 19189T (98.78%). The DNA G+C content was 65.9%. The digital DNA-DNA hybridization and average nucleotide identity values between the isolate strain and aforementioned closely neighbors were low, at 35.8-48.9 and 88.5-92.5%, respectively. Strain YIM B02787T contained Q-8 as the ubiquinone and major fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c, 45.5%) and C16:0 (27.5%). The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unidentified phospholipids, two unidentified aminophospholipids, and one unidentified polar lipid. On the basis of its phylogenetic, phenotypic and chemotaxonomic characteristics, strain YIM B02787Trepresents a novel species of the genus Massilia, for which the name Massilia orientalis sp. nov. is proposed. The type strain is YIM B02787T (= NBRC 116628T = CGMCC 1.61539T).

Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov

Based on genome-wide data, Massilia species belonging to the clade including Telluria mixta LMG 11547T should be entirely transferred to the genus Telluria owing to the nomenclatural priority of the type species Telluria mixta. This results in the transfer of 35 Massilia species to the genus Telluria. The presented data also supports the creation of two new genera since peripherally branching Massilia species are distinct from Telluria and other related genera. It is proposed that 13 Massilia species are transferred to Mokoshia gen. nov. with the type species designated Mokoshia eurypsychrophila comb. nov. The species Massilia arenosa is proposed to belong to the genus Zemynaea gen. nov. as the type species Zemynaea arenosa comb. nov. The genome-wide analysis was well supported by canonical ordination analysis of Enzyme Commission (EC) codes annotated from genomes via pannzer2. This new approach was performed to assess the conclusions of the genome-based data and reduce possible ambiguity in the taxonomic decision making. Cross-validation of EC code data compared within canonical plots validated the reclassifications and correctly visualized the expected genus-level taxonomic relationships. The approach is complementary to genome-wide methodology and could be used for testing sequence alignment based data across genetically related genera. In addition to the proposed broader reclassifications, invalidly described species 'Massilia antibiotica', 'Massilia aromaticivorans', 'Massilia cellulosiltytica' and 'Massilia humi' are described as Telluria antibiotica sp. nov., Telluria aromaticivorans sp. nov., Telluria cellulosilytica sp. nov. and Pseudoduganella humi sp. nov., respectively. In addition, Telluria chitinolytica is reclassified as Pseudoduganella chitinolytica comb. nov. The use of combined genome-wide and annotation descriptors compared using canonical ordination clarifies the taxonomy of Telluria and its sibling genera and provides another way to evaluate complex taxonomic data.

Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat

The McMurdo Dry Valleys of Antarctica experience a range of selective pressures, including extreme seasonal variation in temperature, water and nutrient availability, and UV radiation. Microbial mats in this ecosystem harbor dense concentrations of biomass in an otherwise desolate environment. Microbial inhabitants must mitigate these selective pressures via specialized enzymes, changes to the cellular envelope, and the production of secondary metabolites, such as pigments and osmoprotectants. Here, we describe the isolation and characterization of a Gram-negative, rod-shaped, motile, red-pigmented bacterium, strain DJPM01, from a microbial mat within the Don Juan Pond Basin of Wright Valley. Analysis of strain DJMP01's genome indicates it can be classified as a member of the Massilia frigida species. The genome contains several genes associated with cold and salt tolerance, including multiple RNA helicases, protein chaperones, and cation/proton antiporters. In addition, we identified 17 putative secondary metabolite gene clusters, including a number of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides (RiPPs), among others, and the biosynthesis pathway for the antimicrobial pigment prodigiosin. When cultivated on complex agar, multiple prodiginines, including the antibiotic prodigiosin, 2-methyl-3-propyl-prodiginine, 2-methyl-3-butyl-prodiginine, 2-methyl-3-heptyl-prodiginine, and cycloprodigiosin, were detected by LC-MS. Genome analyses of sequenced members of the Massilia genus indicates prodigiosin production is unique to Antarctic strains. UV-A radiation, an ecological stressor in the Antarctic, was found to significantly decrease the abundance of prodiginines produced by strain DJPM01. Genomic and phenotypic evidence indicates strain DJPM01 can respond to the ecological conditions of the DJP microbial mat, with prodiginines produced under a range of conditions, including extreme UV radiation.

Massilia agrisoli sp. nov., isolated from rhizospheric soil of banana

A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-52^T, was isolated from the rhizospheric soil of a banana plant. Colonies grew at 10-35 °C (optimum, 28 °C), pH 6.0-9.5 (optimum, pH 7.0-7.5), and in the presence of 0-1.0 % NaCl (optimum 0 %). The strain was positive for catalase and oxidase tests, as well as hydrolysis of gelatin, casein, starch and Tween 20. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-52^T clustered together within the genus Massilia. Strain MAHUQ-52^T was closely related to Massilia soli R798^T (98.6 %) and Massilia polaris RP-1-19^T (98.3 %). The novel strain MAHUQ-52^T has a draft genome size of 4 677 454 bp (25 contigs), annotated with 4193 protein-coding genes, 64 tRNA and 19 rRNA genes. The genomic DNA G+C content was 63.0 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-52^T and closely related type strains were ≤88.4 and 35.8 %, respectively. The only respiratory quinone was ubiquinone-8. The major fatty acids were identified as C_16 : 0 and summed feature 3 (C_15 : 0 iso 2-OH and/or C_16 : 1  ω7c). Strain MAHUQ-52^T contained phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as the major polar lipids. On the basis of dDDH and ANI values, as well as genotypic, chemotaxonomic and physiological data, strain MAHUQ-52^T represents a novel species within the genus Massilia, for which the name Massilia agrisoli sp. nov. is proposed, with MAHUQ-52^T (=KACC 21999^T=CGMCC 1.18577^T) as the type strain.

Comparison of Atmospheric and Lithospheric Culturable Bacterial Communities from Two Dissimilar Active Volcanic Sites, Surtsey Island and Fimmvörðuháls Mountain in Iceland

Surface microbes are aerosolized into the atmosphere by wind and events such as dust storms and volcanic eruptions. Before they reach their deposition site, they experience stressful atmospheric conditions which preclude the successful dispersal of a large fraction of cells. In this study, our objectives were to assess and compare the atmospheric and lithospheric bacterial cultivable diversity of two geographically different Icelandic volcanic sites: the island Surtsey and the Fimmvörðuháls mountain, to predict the origin of the culturable microbes from these sites, and to select airborne candidates for further investigation. Using a combination of MALDI Biotyper analysis and partial 16S rRNA gene sequencing, a total of 1162 strains were identified, belonging to 72 species affiliated to 40 genera with potentially 26 new species. The most prevalent phyla identified were Proteobacteria and Actinobacteria. Statistical analysis showed significant differences between atmospheric and lithospheric microbial communities, with distinct communities in Surtsey’s air. By combining the air mass back trajectories and the analysis of the closest representative species of our isolates, we concluded that 85% of our isolates came from the surrounding environments and only 15% from long distances. The taxonomic proportions of the isolates were reflected by the site’s nature and location.

Massilia phyllostachyos sp. nov., Isolated from the Roots of Moso Bamboo in China

A Gram-negative, strictly aerobic, motile, and rod-shaped bacterial strain G4R7^T was isolated from the roots of moso bamboo (Phyllostachys edulis) in Zhejiang, Hangzhou Province, China. After comparing 16S rRNA gene sequences, strain G4R7^T exhibited the highest similarities with Massilia neuiana PTW21^T (98.3%), followed by M. agri K-3-1^T (98.3%), M. consociate CCUG 58010^T (97.7%), M. niastensis 5516S-1^T (97.7%) and M. yuzhufengensis ZD1-4^T (97.6%). The phylogenetic analysis revealed that strain G4R7^T belonged to the genus Massilia. The draft genome of strain G4R7^T was 5.81 Mb, and the G+C content was 64.4%. The average nucleotide identity values between G4R7^T and another related member of the genus Massilia ranged from 76.6 to 87.2%, and the digital DNA-DNA hybridization ranged from 20.7 to 27.9%. Strain G4R7^T grew at 15-37 °C (optimum 25-30 °C) and pH 6.0-9.0 (optimum pH 7.0) in the presence of 0-3% (w/v) NaCl (optimum 0%). The respiratory quinone was Q-8, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and aminophospholipid. The major cellular fatty acids were C_10:0 3OH, C_12:0, C_12:0 2OH, and C_16:0, summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c). As per the data from chemotaxonomic, phylogenetic, and phenotypic evidence, strain G4R7^T represents a new species of genus Massilia, for which the name Massilia phyllostachyos sp. nov. is proposed. The type strain is G4R7^T (=ACCC 61911^T=GDMCC 1.2961^T=JCM 35225^T).

Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov

A group of seven bacterial strains producing blue-purple pigmented colonies on R2A agar was isolated from freshwater samples collected in a deglaciated part of James Ross Island and Eagle Island, Antarctica, from 2017–2019. The isolates were psychrophilic, oligotrophic, resistant to chloramphenicol, and exhibited strong hydrolytic activities. To clarify the taxonomic position of these isolates, a polyphasic taxonomic approach was applied based on sequencing of the 16S rRNA, gyrB and lepA genes, whole-genome sequencing, rep-PCR, MALDI-TOF MS, chemotaxonomy analyses and biotyping. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the entire group are representatives of the genus Massilia. The closest relatives of the reference strain P8398T were Massilia atriviolacea, Massilia violaceinigra, Massilia rubra, Massilia mucilaginosa, Massilia aquatica, Massilia frigida, Massilia glaciei and Massilia eurypsychrophila with a pairwise similarity of 98.6–100% in the 16S rRNA. The subsequent gyrB and lepA sequencing results showed the novelty of the analysed group, and the average nucleotide identity and digital DNA–DNA hybridisation values clearly proved that P8398T represents a distinct Massilia species. After all these results, we nominate a new species with the proposed name Massilia antarctica sp. nov. The type strain is P8398T (= CCM 8941T = LMG 32108T).

Different characteristics of microbial diversity and special functional microbes in rainwater and topsoil before and after 2019 new coronavirus epidemic in Inner Mongolia Grassland

Grassland ecosystems are vital terrestrial ecosystems. As areas sensitive to climate change, they are critical for assessing the effects of global climate change. In China, grasslands account for over 40% of the land area. There is currently limited information on microbial diversity evolution in different grassland areas, particularly microorganisms with ice nucleation activity (INA) and their potential resources with potential influence to regulate regional precipitation and climate. We used Illumina MiSeq to sequence the 16S rRNA V3-V4 hypervariable region and performed a simple droplet freezing experiment to determine the variation in the grassland microbial community species composition and community structure. Rainwater and topsoil samples from the Hulunbuir Grassland in Inner Mongolia collected over three years were characterized. The dominant bacterial genus in the rainwater was Massilia, and the dominant fungus was Cladosporium. Additionally, the dominant bacteria in the soil were Sphingomonas, and the dominant fungus was Gibberella. There were differences in the microbial communities before and after the coronavirus disease epidemic. Pathogenic microorganisms exhibited inconsistent responses to environmental changes. The low relative abundance of known high-INA microorganisms and the higher freezing temperature indicated that unknown high-efficiency biological ice nucleating particles may be present. We found significant differences in species diversity and richness between the rainwater and soil populations in grassland areas by analyzing the sample community structures. Our research results revealed the species composition and structure of the microbiota in grassland ecosystems in China, indicating that environmental media and human activities may affect the microbiota in the grassland area and indicating underlying microorganisms with high INA.

Massilia soli sp. nov., isolated from soil

A Gram-stain-negative, catalase- and oxidase-positive and aerobic bacterium, designated strain R798T, was isolated from soil in South Korea. Cells were motile rods by means of a single polar flagellum. Growth of strain R798T was observed at 15–35 °C (optimum, 25–30 °C), pH 5.0–8.0 (optimum, 6.0) and 0–1.5 % NaCl (optimum, 0.3 %). Strain R798T contained ubiquinone-8 as the sole isoprenoid quinone, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and C16 : 0 as the major fatty acids and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The DNA G+C content of strain R798T calculated from the whole genome sequence was 63.3 mol%. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences revealed that strain R798T formed a distinct phyletic lineage within the genus Massilia . Strain R798T was most closely related to Massilia eurypsychrophila B528-3T with a 98.0 % 16S rRNA gene sequence similarity. Average nucleotide identity and digital DNA–DNA hybridization values between strain R798T and the type strain of M. eurypsychrophila were 79.2 and 22.7 %, respectively. Based on the phenotypic, chemotaxonomic and molecular analyses, strain R798T represents a novel species of the genus Massilia , for which the name Massilia soli sp. nov. is proposed. The type strain is R798T (=KACC 22114T=JCM 34601T).

Massilia puerhi sp. nov., isolated from soil of Pu-erh tea cellar

A Gram-reaction-negative, yellow-pigmented, non-spore-forming rod, aerobic, motile bacterium, designated SJY3^T, was isolated from soil samples collected from a Pu-erh tea cellar in Bolian Pu-erh tea estate Co. Ltd. in Pu'er city, Yunnan, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Massilia. The closest phylogenetic relative was Massilia arenae CICC 24458^T (99.5 %), followed by M. timonae CCUG45783^T (97.9 %), M. oculi CCUG43427A^T (97.8 %), and M. aurea DSM 18055^T (97.8 %). The major fatty acids were C_16 : 0 and C_16 : 1  ω7c and/or C_16 : 1  ω6c. The major respiratory quinone was ubiquinone Q-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Genome sequencing revealed a genome size of 5.97 M bp and a G+C content of 65.4 mol%. Pairwise determined whole genome average nucleotide identity (gANI) values and digital DNA-DNA hybridization (dDDH) values were all below the threshold. Although the 16S rRNA gene similarity of stain SJY3^T and Massilia arenae CICC 24458^T was more than 99 %, the gANI, dDDH values and genomic tree clearly indicated that they were not of the same species. In summary, strain SJY3^T represents a new species, for which we propose the name Massilia puerhi sp. nov. with the type strain SJY3^T (=CGMCC 1.17158^T=KCTC 82193^T).

Cold-shock gene cspC in the genome of Massilia polaris sp. nov. revealed cold-adaptation

A straw coloured, motile and Gram-stain-negative bacterium, designated RP-1-19^T was isolated from soil of Arctic station, Svalbard, Norway. Based on the phylogenetic analysis of its 16S rRNA gene sequence, strain RP-1-19^T formed a lineage within the family Oxalobacteraceae and clustered together within the genus Massilia. The closest members were M. violaceinigra B2^T (98.6% sequence similarity), M. eurypsychrophilia JCM 30074^T (98.3%) and M. atriviolacea SOD^T (98.1%). The only respiratory quinone was ubiquinone-8. The principal cellular fatty acids were summed feature 3 (iso-C_15:0 2-OH/C_16:1ω7c) and C_16:0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain was 63.2%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain RP-1-19^T and closest members were ≤ 80 and 23.2%, respectively. The genome was 4,522,469 bp long with 30 scaffolds and 4076 protein-coding genes. The genome showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Genome analysis revealed the presence of cold-shock proteins CspA and CspC. Presence of cspA and cspC genes in the genome manifest ecophysiology of strain RP-1-19^T that may help in cold-adaptation. Based on these data, strain RP-1-19^T represents a novel species in the genus Massilia, for which the name Massilia polaris sp. nov. is proposed. The type strain is RP-1-19^T (= KACC 21619^T = NBRC 114359^T).

Massilia aromaticivorans sp. nov., a BTEX Degrading Bacterium Isolated from Arctic Soil

A novel BTEX degrading bacterial strain, designated ML15P13^T, was isolated from Arctic soil at the Svalbard Islands, Norway, using an enrichment culture technique. This isolate is Gram-negative, aerobic, motile with multiple flagella at one polar end, and rod-shaped. Growth was observed at 4-35 °C, pH 6.0-8.0, and 0-0.5% (w/v) NaCl. According to 16S rRNA gene analysis, strain ML15P13^T was grouped with members of the genus Massilia and closely related to Massilia atriviolacea SOD^T (98.4%), Massilia violaceinigra B2^T (98.3%), Massilia eurypsychrophila B528-3^T (97.7%), Massilia glaciei B448-2^T (97.7%), and Massilia psychrophila B115-1^T (96.6%). Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity between genome sequences of strain ML15P13^T and the closely related species ranged from 75.8 to 84.3%, from 19.6 ± 1.0 to 21.6 ± 0.3%, and from 68.8 to 71.0%, respectively. The major fatty acids were C_16:0, summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c), and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). Q-8 was the major ubiquinone. The polar lipid profile showed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified phospholipid, and five unidentified polar lipids. The G + C content of the genomic DNA was 64.2 mol%. Based on the results for genotypic and phenotypic study, we conclude that strain ML15P13^T represents a novel species of the genus Massilia, for which the name Massilia aromaticivorans sp. nov. is proposed. The type strain is ML15P13^T (= KACC 21773^T = JCM 34089^T).

Genome insight and description of antibiotic producing Massilia antibiotica sp. nov., isolated from oil-contaminated soil

An ivory-coloured, motile, Gram-stain-negative bacterium, designated TW-1^T was isolated from oil-contaminated experimental soil in Kyonggi University. The phylogenetic analysis based on 16S rRNA gene sequence revealed, strain TW-1^T formed a lineage within the family Oxalobacteraceae and clustered as members of the genus Massilia. The closest members were M. pinisoli T33^T (98.8% sequence similarity), M. putida 6NM-7^T (98.6%), M. arvi THG-RS2O^T (98.5%), M. phosphatilytica 12-OD1^T (98.3%) and M. niastensis 5516S-1^T (98.2%). The sole respiratory quinone is ubiquinone-8. The major cellular fatty acids are hexadeconic acid, cis-9, methylenehexadeconic acid, summed feature 3 and summed feature 8. The major polar lipids are phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain is 66.3%. The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain TW-1^T and closest members were below the threshold value for species demarcation. The genome size is 7,051,197 bp along with 46 contigs and 5,977 protein-coding genes. The genome showed 5 putative biosynthetic gene clusters (BGCs) that are responsible for different secondary metabolites. Cluster 2 showed thiopeptide BGC with no known cluster blast, indicating TW-1^T might produce novel antimicrobial agent. The antimicrobial assessment also showed that strain TW-1^T possessed inhibitory activity against Gram-negative pathogens (Escherichia coli and Pseudomonas aeruginosa). This is the first report of the species in the genus Massilia which produces antimicrobial compounds. Based on the polyphasic study, strain TW-1^T represents novel species in the genus Massilia, for which the name Massilia antibiotica sp. nov. is proposed. The type strain is TW-1^T (= KACC 21627^T = NBRC 114363^T).

Description of Massilia rubra sp. nov., Massilia aquatica sp. nov., Massilia mucilaginosa sp. nov., Massilia frigida sp. nov., and one Massilia genomospecies isolated from Antarctic streams, lakes and regoliths

Bacteria of the genus Massilia often colonize extreme ecosystems, however, a detailed study of the massilias from the Antarctic environment has not yet been performed. Here, sixty-four Gram-stain-negative, aerobic, motile rods isolated from different environmental samples on James Ross Island (Antarctica) were subjected to a polyphasic taxonomic study. The psychrophilic isolates exhibited slowly growing, moderately slimy colonies revealing bold pink-red pigmentation on R2A agar. The set of strains exhibited the highest 16S rRNA gene sequence similarities (99.5-99.9%) to Massilia violaceinigra B2^T and Massilia atriviolacea SOD^T and formed several phylogenetic groups based on the analysis of gyrB and lepA genes. Phenotypic characteristics allowed four of them to be distinguished from each other and from their closest relatives. Compared to the nearest phylogenetic neighbours the set of six genome-sequenced representatives exhibited considerable phylogenetic distance at the whole-genome level. Bioinformatic analysis of the genomic sequences revealed a high number of putative genes involved in oxidative stress response, heavy-metal resistance, bacteriocin production, the presence of putative genes involved in nitrogen metabolism and auxin biosynthesis. The identification of putative genes encoding aromatic dioxygenases suggests the biotechnology potential of the strains. Based on these results four novel species and one genomospecies of the genus Massilia are described and named Massilia rubra sp. nov. (P3094^T=CCM 8692^T=LMG 31213^T), Massilia aquatica sp. nov. (P3165^T=CCM 8693^T=LMG 31211^T), Massilia mucilaginosa sp. nov. (P5902^T=CCM 8733^T=LMG 31210^T), and Massilia frigida sp. nov. (P5534^T=CCM 8695^T=LMG 31212^T).

Bacterial Diversity of a High-Altitude Permafrost Thaw Pond Located on Ojos del Salado (Dry Andes, Altiplano-Atacama Region)

Microbial ecology of permafrost, due to its ecological and astrobiological importance, has been in the focus of studies in past decades. Although permafrost is an ancient and stable environment, it is also subjected to current climate changes. Permafrost degradation often results in generation of thaw ponds, a phenomenon not only reported mainly from polar regions but also present in high-altitude permafrost environments. Our knowledge about microbial communities of thaw ponds in these unique, remote mountain habitats is sparse. This study presents the first culture collection and results of the next-generation DNA sequencing (NGS) analysis of bacterial communities inhabiting a high-altitude permafrost thaw pond. In February 2016, a permafrost thaw pond on the Ojos del Salado at 5900 m a.s.l. (meters above sea level) was sampled as part of the Hungarian Dry Andes Research Programme. A culture collection of 125 isolates was established, containing altogether 11 genera belonging to phyla Bacteroidetes, Actinobacteria, and Proteobacteria. Simplified bacterial communities with a high proportion of candidate and hitherto uncultured bacteria were revealed by Illumina MiSeq NGS. Water of the thaw pond was dominated by Bacteroidetes and Proteobacteria, while in the sediment of the lake and permafrost, members of Acidobacteria, Actinobacteria, Bacteroidetes, Patescibacteria, Proteobacteria, and Verrucomicrobia were abundant. This permafrost habitat can be interesting as a potential Mars analog.

Massilia arenae sp. nov., isolated from sand soil in the Qinghai–Tibetan Plateau

A bacterial strain, designated GEM5T, was isolated from sand soil samples from the Qinghai–Tibet Plateau. The polyphasic study confirmed the affiliation of the isolate with the genus Massilia . GEM5T had Gram-stain-negative, non-spore-forming and rod-shaped cells and grew at 4–30 °C, pH 6–8 and with 0–2 % (w/v) NaCl. Its cell wall contained ribose. Q8 was the predominant respiratory quinone, and summed feature 3 (C16 : 1ω6c/ω7c) and C16 : 0 were the major components of the fatty acids. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and four unidentified lipids. The DNA G+C content was 65.1 mol%. The phylogenetic analysis based on the 16S rRNA gene showed a stable clade being formed by GEM5T, Massilia timonae CCUG 45783T (97.94 %) and Massilia oculi CCUG 43427AT (97.58 %). The average nucleotide identity (ANIb) values between GEM5T and M. timonae CCUG 45783T, M.oculi CCUG 43427AT were 91.3 and 91.7 %, respectively. On the basis of the morphological, physiological and chemotaxonomic pattern, it was proposed that strain GEM5T (=JCM 32744T=CICC 24458T) should be classified as representing a member of the genus Massilia with the name Massilia arenae sp. nov.

Fungal and bacterial diversity of Svalbard subglacial ice

The composition of fungal and bacterial communities in three polythermal glaciers and associated aquatic environments in Kongsfjorden, Svalbard was analysed using a combination of cultivation and amplicon sequencing. 109 fungal strains belonging to 30 mostly basidiomycetous species were isolated from glacial samples with counts up to 10³ CFU/100 ml. Glaciozyma-related taxon and Phenoliferia psychrophenolica were the dominant species. Unexpectedly, amplicon sequencing uncovered sequences of Chytridiomycota in all samples and Rozellomycota in sea water, lake water, and tap water. Sequences of Malassezia restricta and of the extremely halotolerant Hortaea werneckii were also found in subglacial habitats for the first time. Overall, the fungal communities within a glacier and among glaciers were diverse and spatially heterogenous. Contrary to this, there was a large overlap between the bacterial communities of different glaciers, with Flavobacterium sp. being the most frequently isolated. In amplicon sequencing Actinobacteria and Proteobacteria sequences were the most abundant.

Total and Potentially Active Bacterial Communities Entrapped in a Late Glacial Through Holocene Ice Core From Scarisoara Ice Cave, Romania

Our understanding of the icy-habitat microbiome is likely limited by a lack of reliable data on microorganisms inhabiting underground ice that has accumulated inside caves. To characterize how environmental variation impacts cave ice microbial community structure, we determined the composition of total and potentially active bacterial communities along a 13,000-year-old ice core from Scarisoara cave (Romania) through 16S rRNA gene Illumina sequencing. An average of 2,546 prokaryotic gDNA operational taxonomic units (OTUs) and 585 cDNA OTUs were identified across the perennial cave ice block and analyzed in relation to the geochemical composition of ice layers. The total microbial community and the putative active fraction displayed dissimilar taxa profiles. The ice-contained microbiome was dominated by Actinobacteria with a variable representation of Proteobacteria, while the putative active microbial community was equally shared between Proteobacteria and Firmicutes. Accordingly, a major presence of Cryobacterium, Lysinomonas, Pedobacter, and Aeromicrobium phylotypes homologous to psychrotrophic and psychrophilic bacteria from various cold environments were noted in the total community, while the prevalent putative active bacteria belonged to Clostridium, Pseudomonas, Janthinobacterium, Stenotrophomonas, and Massilia genera. Variation in the microbial cell density of ice strata with the dissolved organic carbon (DOC) content and the strong correlation of DOC and silicon concentrations revealed a major impact of depositional processes on microbial abundance throughout the ice block. Post-depositional processes appeared to occur mostly during the 4,000–7,000 years BP interval. A major bacterial composition shift was observed in 4,500–5,000-year-old ice, leading to a high representation of Beta- and Deltaproteobacteria in the potentially active community in response to the increased concentrations of DOC and major chemical elements. Estimated metabolic rates suggested the presence of a viable microbial community within the cave ice block, characterized by a maintenance metabolism in most strata and growth capacity in those ice deposits with high microbial abundance and DOC content. This first survey of microbial distribution in perennial cave ice formed since the Last Glacial period revealed a complex potentially active community, highlighting major shifts in community composition associated with geochemical changes that took place during climatic events that occurred about 5,000 years ago, with putative formation of photosynthetic biofilms.

Massilia atriviolacea sp. nov., a dark purple-pigmented bacterium isolated from soil

A bacterial strain, designated SOD^T, with Gram-stain-negative and motile rod-shaped cells, was isolated from soil in Hefei, PR China, and was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SOD^T belonged to the genus Massilia and showed the highest similarities to Massilia violaceinigra B2^T (99.3 %), followed by Massilia glaciei B448-2^T (98.7 %), Massilia eurypsychrophila CGMCC 1.12828^T (98.6 %) and Rugamonas rubra CCM3730^T (97.8 %). Average nucleotide identity and digital DNA-DNA hybridization values between genome sequences of strain SOD^T and the closely related species ranged from 77.1 to 89.3% and from 22.2 to 34.7 %. The DNA G+C content of strain SOD^T was 65.4 mol%. Strain SOD^T contained Q-8 as the major ubiquinone and the dominant fatty acids were summed feature 3 (C16 : 1ω7c and/or C15 : 0iso 2-OH; 58.5 %), C16 : 0 (26.8 %) and C18 : 1ω7c (5.0 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. On the basis of the evidence presented in this study, strain SOD^T represents a novel species of the genus Massilia, for which the name Massiliaatriviolacea sp. nov. is proposed. The type strain is SOD^T (=KCTC 62720^T=LMG 30840^T).

Low-Temperature Sulfidic-Ice Microbial Communities, Borup Fiord Pass, Canadian High Arctic

A sulfur-dominated supraglacial spring system found at Borup Fiord Pass (BFP), Ellesmere Island, Nunavut, Canada, is a unique sulfur-on-ice system expressed along the toe of a glacier. BFP has an intermittent flowing, subsurface-derived, glacial spring that creates a large white-yellow icing (aufeis) that extends down-valley. Over field campaigns in 2014, 2016, and 2017, numerous samples were collected and analyzed for both microbial community composition and aqueous geochemistry. Samples were collected from multiple site types: spring discharge fluid, aufeis (spring-derived ice), melt pools with sedimented cryoconite material, and mineral precipitate scrapings, to probe how microbial communities differed between site types in a dynamic freeze/thaw sulfur-rich system. Dissolved sulfate varied between 0.07 and 11.6 mM and was correlated with chloride concentrations, where the fluids were saltiest among spring fluids. The highest sulfate samples exhibited high dissolved sulfide values between 0.22 and 2.25 mM. 16S rRNA gene sequencing from melt pool and aufeis samples from the 2014 campaign were highly abundant in operational taxonomic units (OTUs) closely related to sulfur-oxidizing microorganisms (SOM; Sulfurimonas, Sulfurovum, and Sulfuricurvum). Subsequent sampling 2 weeks later had fewer SOMs and showed an increased abundance of the genus Flavobacterium. Desulfocapsa, an organism that specializes in the disproportionation of inorganic sulfur compounds was also found. Samples from 2016 and 2017 revealed that microorganisms present were highly similar in community composition to 2014 samples, primarily echoed by the continued presence of Flavobacterium sp. Results suggest that while there may be acute events where sulfur cycling organisms dominate, a basal community structure appears to dominate over time and site type. These results further enhance our knowledge of low-temperature sulfur systems on Earth, and help to guide the search for potential life on extraterrestrial worlds, such as Europa, where similar low-temperature sulfur-rich conditions may exist.

Massilia violaceinigra sp. nov., a novel purple-pigmented bacterium isolated from glacier permafrost

A Gram-stain-negative, motile and rod-shaped bacterium, designated strain B2^T, which can synthesize purple pigments of violacein and dexyoviolacein, was isolated from Tianshan glacier in Xinjiang, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that it was grouped in the genus Massilia with Massilia glaciei B448-2^T, Massilia eurypsychrophila B528-3^T and Massilia psychrophila B1555-1^T as its closest relatives (98.2, 97.9 and 97.0 % 16S rRNA gene sequence similarity, respectively). Genomic relatedness between strain B2^T and its closest relatives was evaluated using average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity, with values of 77.93-85.08 %, 22.4-23.4 % and 71.54-72.99 %, respectively. Q-8 was the major ubiquinone. The major fatty acids (>5 %) of strain B2^T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C12 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids included phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain B2^T was 63.51 mol%. Based on genomic relatedness, physiological, biochemical and chemotaxonomic data, strain B2^T (=CGMCC 1.6993^T=DSM 19531^T=KCTC 32446^T) is considered to represent a novel species within the genus Massilia, for which the name Massilia violaceinigra sp. nov. is proposed.

Massilia neuiana sp. nov., isolated from wet soil

A novel aerobic, Gram-stain-negative, rod-shaped, motile bacterium, strain PTW21^T, was isolated from wet soil. 16S rRNA gene sequence phylogenetic analysis of strain PTW21^T revealed an affiliation to the genus Massilia and it shared 98.5 and 98.1 % similarity with Massilianiastensis 5516 S-1^T and Massilia tieshanensis TS3^T, respectively. Growth occurred at 10-45 °C, pH 4.5-12.5 and NaCl concentrations up to 2 % (w/v). The major fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. The predominant respiratory quinone was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain PTW21^T was 64.6 mol%. The results of DNA-DNA hybridization revealed that strain PTW21^T showed 37.4 % relatedness with Massilia niastensis 5516 S-1^T and 40.0 % with M. tieshanensis TS3^T. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain PTW21^T (=CICC 24113^T=BCRC 81061^T) is proposed as the type strain of novel species of the genus Massilia with the names Massilia neuiana sp. nov.

Massilia phosphatilytica sp. nov., a phosphate solubilizing bacteria isolated from a long-term fertilized soil

A Gram-stain-negative and rod-shaped bacterial strain, 12-OD1T, with rock phosphate solubilizing ability was isolated from agricultural soil in Hailun, Heilongjiang, PR China. The isolate was affiliated to the genus Massilia, based on 16S rRNA gene sequence alignments, having the highest similarities with Massilia putida6 NM-7T (98.67 %), Massilia kyonggiensis TSA1T (98.28 %), and Massilia norwichensis NS9T (98.07 %), respectively. The DNA G+C content was 67.72 mol% and DNA-DNA hybridization showed low relatedness values (less than 47 %) between strain 12-OD1T and other phylogenetically related species of the genus Massilia. The predominant isoprenoid quinone was Q-8 and the polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C17 : 0 cyclo (25.4 %), C16 : 0 (23.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1 ω6c) (22.5 %), which differentiates it from close relatives within the genus Massilia. Combined genetic, physiological and biochemical properties indicate that strain 12-OD1T is a novel species of the genus Massilia, for which the name Massilia phosphatilytica sp. nov., is proposed, with the type strain 12-OD1T (=CCTCC AB 2016251T=LMG 29956T=KCTC 52513T).

Massilia glaciei sp. nov., isolated from the Muztagh Glacier

A Gram-stain-negative, rod-shaped, bacterial strain, B448-2^T, was isolated from an ice core from the Muztagh Glacier, on the Tibetan Plateau. B448-2^T grew optimally at pH 7.0 and 20 °C in the presence of 0-1.0 % (w/v) NaCl. The results of 16S rRNA gene sequence similarity analysis indicated that B448-2^T was closely related to Massilia eurypsychrophila CGMCC 1.12828^T, Rugamonas rubra CCM3730^T and Duganella zoogloeoides JCM20729^T at levels of 97.8, 97.7  and 97.3 %, respectively. The predominant fatty acids of B448-2^T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The predominant isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of the strain was 66.1 mol%. In DNA-DNA hybridization tests, B448-2^T shared 37.6 % DNA-DNA relatedness with Massilia eurypsychrophila CGMCC 1.12828^T. On the basis of the results for phenotypic and chemotaxonomic characteristics, B448-2^T was considered to represent a novel species of the genus Massilia, for which the name Massiliaglaciei sp. nov. is proposed. The type strain is B448-2^T (=JCM 30271^T=CGMCC 1.12920^T).

Comparative analysis of bacteria associated with different mosses by 16S rRNA and 16S rDNA sequencing

To understand the differences of the bacteria associated with different mosses, a phylogenetic study of bacterial communities in three mosses was carried out based on 16S rDNA and 16S rRNA sequencing. The mosses used were Hygroamblystegium noterophilum, Entodon compressus and Grimmia montana, representing hygrophyte, shady plant and xerophyte, respectively. In total, the operational taxonomic units (OTUs), richness and diversity were different regardless of the moss species and the library level. All the examined 1183 clones were assigned to 248 OTUs, 56 genera were assigned in rDNA libraries and 23 genera were determined at the rRNA level. Proteobacteria and Bacteroidetes were considered as the most dominant phyla in all the libraries, whereas abundant Actinobacteria and Acidobacteria were detected in the rDNA library of Entodon compressus and approximately 24.7% clones were assigned to Candidate division TM7 in Grimmia montana at rRNA level. The heatmap showed the bacterial profiles derived from rRNA and rDNA were partly overlapping. However, the principle component analysis of all the profiles derived from rDNA showed sharper differences between the different mosses than that of rRNA-based profiles. This suggests that the metabolically active bacterial compositions in different mosses were more phylogenetically similar and the differences of the bacteria associated with different mosses were mainly detected at the rDNA level. Obtained results clearly demonstrate that combination of 16S rDNA and 16S rRNA sequencing is preferred approach to have a good understanding on the constitution of the microbial communities in mosses.

Massilia psychrophila sp. nov., isolated from an ice core

A Gram-stain-negative, aerobic, rod-shaped, motile bacterium, strain B1555-1T, was isolated from an ice core drilled from Ulugh Muztagh Glacier, China. The optimum growth temperature of strain B1555-1T was 15 °C and optimum pH was 7. The major fatty acids of strain B1555-1T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The predominant respiratory quinone was Q-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain B1555-1T was 66.0 mol%. In 16S rRNA gene sequence comparisons, strain B1555-1T was affiliated to the genus Massilia and shared 98.30 and 97.13 % similarity with Massilia eurypsychrophila B528-3T and Massilia niabensis 5420S-26T, respectively. The results of DNA-DNA hybridization revealed that strain B1555-1T showed 49.8 % relatedness with M. eurypsychrophila B528-3T and 38.5 % with M. niabensis 5420S-26T. Based on the genotypic and phenotypic evidence presented in this study, strain B1555-1T represents a novel species of the genus Massilia, for which the name Massilia psychrophila sp. nov. is proposed. The type strain is B1555-1T (=CGMCC 1.15196T=JCM 30813T).

Massilia putida sp. nov., a dimethyl disulfide-producing bacterium isolated from wolfram mine tailing

A heavy metal-resistant and dimethyl disulfide-producing bacterial strain, designated 6NM-7T, was isolated from wolfram mine tailing, Dayu County, Jiangxi Province, PR China. Strain 6NM-7T was aerobic, Gram-stain-negative and motile by means of a single polar flagellum. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain 6NM-7T was affiliated with the genus Massilia and was closely related to Massilia norwichensis LMG 28164T (98.8 % 16S rRNA gene sequence similarity), Massilia kyonggiensis KACC 17471T (98.4 %), Massilia niastensis KACC 12599T (97.8 %), Massilia tieshanensis KACC 14940T (97.3 %), Massilia haematophila KACC 13771T (97.2 %), Massilia namucuonensis CGMCC 1.11014T (97.1 %) and Massilia aerilata KACC 12505T (97.1 %). The DNA-DNA relatedness values between strain 6NM-7T and its closely related type strains were all below 70 %. The major respiratory quinone was unbiquinone 8 (Q-8) and the major cellular fatty acids consisted of C16 : 0 (33.2 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 21.8 %), C17 : 0 cyclo (20.8 %), C18 : 1ω7c (7.4 %) and C10 : 0 3-OH (5.8 %). The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of strain 6NM-7T was 66.8 ± 0.6 mol%. On the basis of the results of this polyphasic taxonomic study, strain 6NM-7T should be assigned to a novel species of the genus Massilia, for which the name Massilia putida sp. nov. is proposed. The type strain is 6NM-7T ( = DSM 27523T = KCTC 42761T).