Cohnella formosensis sp. nov., a xylanolytic bacterium isolated from the rhizosphere of Medicago sativa L

Description of Cohnella rhizoplanae sp. nov., isolated from the root surface of soybean (Glycine max)

A Gram-staining-positive, aerobic bacterium, designated strain JJ-181 T, was isolated from the root surface of soybean. Based on the 16S rRNA gene sequence similarities, strain JJ-181 T was grouped into the genus Cohnella, most closely related to Cohnella hashimotonis F6_2S_P_1T (98.85%) and C. ginsengisoli GR21-5 T (98.3%). The pairwise average nucleotide identity and digital DNA-DNA hybridisation values of the JJ-181 T genome assembly against publicly available Cohnella type strain genomes were below 84% and 28%, respectively. The fatty acid profile from whole cell hydrolysates, the cell wall diaminoacid, the quinone system, the polar lipid profile, and the polyamine pattern supported the allocation of strain JJ-181 T to the genus Cohnella. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain JJ-181 T from its closely-related Cohnella species. Functional analysis revealed that strain JJ-181 T has different gene clusters related to swarming motility, chemotaxis ability, and endospore and biofilm formations. The gene content also suggests the ability of strain JJ-181 T to synthesise biotin and riboflavin, as well as indole-3-acetic acid, an important phytohormone for plant growth. Based on polyphasic analyses, strain JJ-181 T can be classified as a new species of the genus Cohnella, for which we propose the name Cohnella rhizoplanae sp. nov., with strain JJ-181 T (= LMG 31678 T = CIP 112018 T = CCM 9031 T = DSM 110650 T) as the type strain.

Comparative genomic analysis of Cohnella hashimotonis sp. nov. isolated from the International Space Station

A single strain from the family Paenibacillaceae was isolated from the wall behind the Waste Hygiene Compartment aboard the International Space Station (ISS) in April 2018, as part of the Microbial Tracking mission series. This strain was identified as a gram-positive, rod-shaped, oxidase-positive, catalase-negative motile bacterium in the genus Cohnella, designated as F6_2S_P_1T. The 16S sequence of the F6_2S_P_1T strain places it in a clade with C. rhizosphaerae and C. ginsengisoli, which were originally isolated from plant tissue or rhizosphere environments. The closest 16S and gyrB matches to strain F6_2S_P_1T are to C. rhizosphaerae with 98.84 and 93.99% sequence similarity, while a core single-copy gene phylogeny from all publicly available Cohnella genomes places it as more closely related to C. ginsengisoli. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values to any described Cohnella species are <89 and <22%, respectively. The major fatty acids for strain F6_2S_P_1T are anteiso-C15:0 (51.7%), iso-C16:0 (23.1%), and iso-C15:0 (10.5%), and it is able to metabolize a wide range of carbon compounds. Given the results of the ANI and dDDH analyses, this ISS strain is a novel species within the genus Cohnella for which we propose the name Cohnella hashimotonis, with the type strain F6_2S_P_1T (=NRRL B-65657T and DSMZ 115098T). Because no closely related Cohnella genomes were available, this study generated the whole-genome sequences (WGSs) of the type strains for C. rhizosphaerae and C. ginsengisoli. Phylogenetic and pangenomic analysis reveals that F6_2S_P_1T, C. rhizosphaerae, and C. ginsengisoli, along with two uncharacterized Cohnella strains, possess a shared set of 332 gene clusters which are not shared with any other WGS of Cohnella species, and form a distinct clade branching off from C. nanjingensis. Functional traits were predicted for the genomes of strain F6_2S_P_1T and other members of this clade.

Cohnella terricola sp. nov., isolated from soil

A Gram-positive, aerobic, flagellated, endospore-forming, rod-shaped strain, designated as G13^T, was isolated from soil. The results of 16S rRNA gene sequence analysis led to the conclusion that strain G13^T was phylogenetically related to Cohnella boryungensis BR29^T (97.5 %) and Cohnella phaseoli CECT 7287^T (96.9 %) with digital DNA-DNA hybridization values of 21.0 and 21.4 %, and distantly related to Cohnella thermotolerans CCUG 47242^T (94.8 %), type species of the genus Cohnella, at 19.0 %. The genome size of strain G13^T was 5 387 258 bp, with 51.3 mol% G+C content. The predominant fatty acids were summed feature 9 (iso-C_17 : 1  ω9c and/or C_16 : 0 10-methyl), anteiso-C_17 : 0, iso-C_17 : 0 and iso-C_15 : 0. The predominant quinone was menaquinone-7 and the major polar lipids were diphosphatidyglycerol, phosphatidylethanolamine, phosphatidylglycerol, lysylphosphatidylglycerol, three aminophospholipids, two phosphoglycolipids, three aminolipids and two unidentified lipids. Based on the data from phenotypic tests and the genotypic differences between strain G13^T and its close phylogenetic relatives, strain G13^T represents a new species belonging to the genus Cohnella, for which the name Cohnella terricola sp. nov. (=KACC 19905^T=NBRC 113748^T) is proposed.

Cohnella pontilimi sp. nov., isolated from tidal-flat mud

A Gram-positive, aerobic, endospore-forming, rod-shaped bacterial strain, CAU 1483 ^T, was isolated from tidal-flat mud in the Republic of Korea. It grew optimally at 30 °C, in a pH 7.0 medium with 2% (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1483 ^T formed a separate clade within Paenibacillaceae together with members of the genus Cohnella. Strain CAU 1483 ^T exhibited the highest 16S rRNA gene sequence similarity (97.1%) to C. candidum 18JY8-7 ^T. Whole genome of strain CAU 1483 ^T was 4.29 Mb in size with a 53.7 mol% G + C content, and included 4046 coding sequences and included 4046 coding sequences, some of which associated with stress response. The average nucleotide identity and digital DNA-DNA hybridization similarity between strain CAU 1483 ^T and related members of the genus Cohnella were 71.8-74.9% and 22.6-33.9%, respectively. The major respiratory quinone present in this strain was menaquinone-7. Strain CAU 1483 ^T contained anteiso-C_15:0 and iso-C_16:0 as the major fatty acids, while its polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, lysyl-phosphatidylglycerol, phosphatidylcholine, three unidentified aminophospholipids, two unidentified lipids and an unidentified phospholipid. Peptidoglycan type was A1γ meso-Dpm. On the basis of taxonomic characterization, strain CAU 1483 ^T constitutes a novel species, for which the name Cohnella pontilimi sp. nov. is proposed. The type strain of this novel species is CAU 1483 ^T (= KCTC 43047 ^T = NBRC 113953 ^T).

Description of Cohnella zeiphila sp. nov., a bacterium isolated from maize callus cultures

A Gram-stain positive, aerobic, motile, rod-shaped bacterium designated as strain CBP-2801^T was isolated as a contaminant from a culture containing maize callus in Peoria, Illinois, United States. The strain is unique relative to other Cohnella species due to its slow growth and reduced number of sole carbon sources. Phylogenetic analysis using 16S rRNA indicated that strain CBP-2801^T is a Cohnella bacterium and showed the highest similarity to Cohnella xylanilytica (96.8%). Genome-based phylogeny and genomic comparisons based on average nucleotide identity confirmed the strain to be a novel species of Cohnella. Growth occurs at 15-45 °C (optimum 40 °C), pH 5-7 (optimum pH 6) and with 0-1% NaCl. The predominant fatty acids are anteiso-15:0 and 18:1 ω6c. Genome mining for secondary metabolites identified a putative biosynthetic cluster that encodes for a novel lasso peptide. In addition, this study contributes five new genome assemblies of type strains of Cohnella species, a genus with less than 30% of the type strains sequenced. The DNA G + C content is 58.7 mol %. Based on the phenotypic, phylogenetic and biochemical data strain CBP-2801^T represents a novel species, for which the name Cohnella zeiphila sp. nov. is proposed. The type strain is CBP-2801^T (= DSM 111598 = ATCC TSD-230).

Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion

(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.

Cohnella fermenti sp. nov., isolated from a fermentation process

A novel Gram-stain-positive, aerobic, motile with peritrichous flagella, rod-shaped bacterium, designated CC-MHH1044^T, was isolated from a preserved vegetable sample. A polyphasic taxonomic approach was applied to the isolates in order to clarify its taxonomic position. Growth of the strain CC-MHH1044^T occurred at 15-50 °C (optimum, 30 °C), pH 6.0-8.0 (optimum, pH 7.0) and with 0-2.0 % (w/v) NaCl (optimum, 1 %, w/v). The genome of strain CC-MHH1044^T consisted of 8.5 Mb and the genomic DNA G+C content was 58.5 mol%. Comparison of the 16S rRNA gene sequences showed that CC-MHH1044^T belonged to the genus Cohnella and showed a close relationship with the type strains of Cohnella damuensis (96.2 %) and Cohnella panacarvi (95.9 %), and lower sequence similarity to other species. Average nucleotide identity values calculated from whole-genome sequencing data proved that CC-MHH1044^T represents a distinct Cohnella species. The dominant cellular fatty acids (>5 %) included iso-C_14 : 0(7.4 %), iso-C_15 : 0 (6.4 %), anteiso-C_15 : 0(40.3 %), C_16 : 0 (6.6 %) and iso-C_16 : 0 (27.0 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids, one unidentified phospholipid and glycolipid. The major polyamine was spermidine. The predominant isoprenoid quinone was menaqinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits, together with results of comparative 16S rRNA gene sequence, average nucleotide identity and digital DNA-DNA hybridization analyses, we conclude that strain CC-MHH1044^T represents a novel member of the genus Cohnella, for which the name Cohnella fermenti sp. nov. is proposed. The type strain is CC-MHH1044^T (=BCRC 81147^T=JCM 32834^T).

Cohnella faecalis sp. nov., isolated from animal faeces in a karst cave

A Gram-stain-positive, rod-shaped, endospore-forming, motile and aerobic bacterial isolate, designated strain K2E09-144^T, was obtained from animal faeces that were collected from a karst cave in Guizhou province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain K2E09-144^T represents a novel member of the genus Cohnella within the family Paenibacillaceae of the phylum Firmicutes. Strain K2E09-144^T was phylogenetically closely related to Cohnella nanjingensis D45^T (16S rRNA gene sequence similarity 97.0 %). The major cellular fatty acids were anteiso-C15:0, iso-C16:0 and C16 : 0. The major isoprenoid quinone was menaqinone 7 (MK-7). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified phospholipid, four unidentified aminophospholipids, one glycolipid and one unidentified lipid. The isomer type of diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The genome of strain K2E09-144^T comprised 6.43 Mb, and encoded 6029 genes in total. The DNA G+C content of the genomic DNA was 53.3 mol%. Based on its phylogenetic, phenotypic and chemotaxonomic characteristics, strain K2E09-144^T is considered to represent a novel species of the genus Cohnella, for which the name Cohnella faecalis sp. nov. is proposed. The type strain is K2E09-144^T (=CGMCC 1.13587^T=NBRC 113454^T).

Agrowastes as Feedstock for the Production of Endo-β-Xylanase from sp. Strain AR92

Members of <i>Cohnella </i>sp. isolated from a variety of environments have been shown to be glycoside hydrolase producers. Nevertheless, most evaluations of members of this genus are limited to their taxonomic description. The strain AR92, previously identified as belonging to the genus <i>Cohnella</i>, formed a well-supported cluster with <i>C. thailandensis</i> and <i>C. formosensis</i> (>80% bootstrap confidence). Its growth and xylanase production were approached by using a mineral-based medium containing alkali-pretreated sugarcane bagasse as the main carbon source, which was assayed as a convenient source to produce biocatalysts potentially fitting its degradation. By means of a two-step statistical approach, the production of endoxylanase was moderately improved (20%). However, a far more significant improvement was observed (145%), by increasing the inoculum size and lowering the fermentation temperature to 25°C, which is below the optimal growth temperature of the strain AR92 (37°C). The xylanolytic preparation produced by <i>Cohnella</i> sp. AR92 contained mild temperature-active endoxylanase (identified as redundant GH10 family) for the main activity which resulted in xylobiose and xylo-oligosaccharides as the main products from birchwood xylan.

Cohnella algarum sp. nov., isolated from a freshwater green alga Paulinella chromatophora

A Gram-stain-positive, facultatively aerobic and endospore-forming bacterium, designated strain Pch-40^T, was isolated from a freshwater green alga, Paulinella chromatophora. Cells were motile rods with a monotrichous polar flagellum showing catalase- and oxidase-positive reactions. Strain Pch-40^T grew at 20-50 °C (optimum, 37-40 °C), at pH 5.0-11.0 (optimum, pH 7.0) and in the presence of 0-4.0 % (w/v) NaCl (optimum, 0 %). Menaquinone-7 was detected as the sole isoprenoid quinone. The genomic DNA G+C content of strain Pch-40^T was 55.6 mol%. The major cellular fatty acids of strain Pch-40^T were C16 : 0, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Pch-40^T clearly belonged to the genus Cohnella of the family Paenibacillaceae. Strain Pch-40^T was most closely related to Cohnella rhizosphaerae CSE-5610^T with a 96.1 % 16S rRNA gene sequence similarity. The phenotypic and chemotaxonomic features and the phylogenetic inference clearly suggested that strain Pch-40^T represents a novel species of the genus Cohnella, for which the name Cohnellaalgarum sp. nov. is proposed. The type strain is strain Pch-40^T (=KACC 19279^T=JCM 32033^T).

Cohnella lubricantis sp. nov., isolated from a coolant lubricant solution

A Gram-stain-positive, aerobic, non-endospore-forming organism, isolated from a coolant lubricant solution was studied for its taxonomic position. On the basis of 16S rRNA gene sequence similarity comparisons, strain KSS-154-50T was grouped into the genus Cohnella, most closely related to Cohnella formosensisCC-ALFALFA-35T (97.3 % 16S rRNA gene sequence similarity), Cohnella rhizosphaerae CSE-5610T (97.1 %) and Cohnella nanjingensis D45T (97.0 %); the 16S rRNA gene sequence similarity to other species of the genus Cohnella was <97.0 %. The fatty acid profile from whole cell hydrolysates was very similar to those reported for other species of the genus Cohnella and supported the allocation to the genus Cohnella. In the fatty acid profiles, iso- and anteiso-branched fatty acids were found as major compounds. The quinone system consisted predominantly of menaquinone MK-7. The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The major polyamine is spermidine. The results of physiological and biochemical characterization allowed in addition a phenotypic differentiation of strain KSS-154-50T from the three most closely related species. Hence, strain KSS-154-50T represents a novel species of the genus Cohnella, for which the name Cohnella lubricantis sp. nov. is proposed. The type strain is KSS-154-50T (=LMG 29763T=CCM 8707T).

Cohnella collisoli sp. nov., isolated from lava forest soil

A novel bacterial strain, NKM-5T, was isolated from soil of a lava forest in Nokkome Oreum, Jeju, Republic of Korea. Cells of strain NKM-5T were Gram-stain-positive, motile, endospore-forming, rod-shaped and oxidase- and catalase-positive. Strain NKM-5T contained anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids; menaquinone-7 (MK-7) as the predominant isoprenoid quinone; diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysyl-phosphatidylglycerol, an unidentified phospholipid and three unidentified aminophospholipids as the polar lipids; and meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C content was 48.3 mol%. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that strain NKM-5T was most closely related to Cohnella lupini RLAHU4BT (96.9 % sequence similarity) and fell into a clade in the genus Cohnella. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain NKM-5T represents a novel species of the genus Cohnella, for which the name Cohnella collisoli sp. nov. is proposed. The type strain is NKM-5T ( = KCTC 33634T = CECT 8805T).

Ammoniibacillus agariperforans gen. nov., sp. nov., a thermophilic, agar-degrading bacterium isolated from compost

A thermophilic, agar-degrading bacterium, strain FAB2(T), was isolated from sewage sludge compost. According to phylogenetic analysis based on 16S rRNA gene sequences, strain FAB2(T) belonged to the family Paenibacillaceae within the phylum Firmicutes. However, FAB2(T) was different enough at the genus level from closely related species. The percentages of 16S rRNA gene sequence similarity with related organisms were 90.4 % for Thermobacillus xylanilyticus, 91.8 % for Paenibacillus barengoltzii, 89.4 % for Cohnella lupini, 90.1 % for Fontibacillus aquaticus, and 89.0 % for Saccharibacillus sacchari. Morphological and physiological analyses revealed that the strain was motile, rod-shaped, Gram-stain-positive, aerobic and able to form oval endospores in swollen sporangia. Ammonium was required as a nitrogen source while nitrate, nitrite, urea and glutamate were not utilized. Catalase and oxidase activities were weakly positive and positive, respectively. The bacterium grew in the temperature range of 50-65 °C and in media with pH 7.5 to 9.0. Optimal growth occurred at 60 °C and pH 8.0-8.6. Growth was inhibited at pH≤7.0 and NaCl concentrations ≥2.5 % (w/v). In chemotaxonomic characterization, MK-7 was identified as the dominant menaquinone. Major fatty acids were iso-C16 : 0 and C16 : 0. Dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phosphatidylcholine was present in a moderate amount. The diamino acid in the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 49.5 mol% in a nucleic acid study. On the basis of genetic and phenotypic characteristics, strain FAB2(T) ( = NBRC 109510(T) = KCTC 33130(T)) showed characteristics suitable for classification as the type strain of a novel species of a new genus in the family Paenibacillaceae, for which the name Ammoniibacillus agariperforans gen. nov., sp. nov. is proposed.

Cohnella nanjingensis sp. nov., an extracellular polysaccharide-producing bacterium isolated from soil

A Gram-stain-positive, rod-shaped, endospore-forming bacterium, strain D45T, was isolated from soil in Nanjing, China. The organism grew optimally at 30 °C, pH 7.0 and with 0 % NaCl (w/v). The 16S rRNA gene sequence of the isolate showed similarities lower than 97 % with respect to species of the genus Cohnella . The predominant respiratory quinone was MK-7, with MK-6 present as a minor component; anteiso-C15 : 0 and iso-C16 : 0 were the major fatty acids. The polar lipids of strain D45T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, four phospholipids, two glycolipids, one aminolipid and two lipids. The DNA G+C content was 59.5 mol%. DNA–DNA hybridization of the isolate with two reference strains showed relatedness values of 33.4 % with Cohnella ginsengisoli DSM 18997T and 25.8 % with Cohnella thermotolerans DSM 17683T. The phylogenetic, chemotaxonomic and phenotypic data supported the classification of strain D45T as a representative of a novel species of the genus Cohnella , for which the name Cohnella nanjingensis sp. nov. is proposed. The type strain is D45T ( = CCTCC AB 2014067T = DSM 28246T).

Cohnella rhizosphaerae sp. nov., isolated from the rhizosphere environment of Zea mays

A Gram-staining-positive, aerobic, non-endospore forming organism, isolated as a seed endophyte (colonizing the internal healthy tissue of plant seed) of sweet corn (Zea mays), strain CSE-5610T, was studied for its taxonomic allocation. On the basis of 16S rRNA gene sequence comparisons, strain CSE-5610T was grouped into the genus Cohnella, most closely related to Cohnella ginsengisoli GR21-5T (98.1%) and 'Cohnella plantaginis' YN-83 (97.5%). The 16S rRNA gene sequence similarity to other members of the genus Cohnella was <96.6%. DNA-DNA hybridization of strain CSE-5610T with C. ginsengisoli DSM 18997T and 'C. plantaginis' DSM 25424 was 58% (reciprocal 24%) and 30% (reciprocal 27%), respectively. The fatty acid profile from whole cell hydrolysates supported the allocation of the strain to the genus Cohnella; iso- and anteiso-branched fatty acids were found as major compounds. meso-Diaminopimelic acid was identified as the cell-wall diamino acid. The quinone system consisted predominantly of menaquinone MK-7. The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, a phospholipid and minor amounts of two polar lipids. In the polyamine pattern, spermidine was the major polyamine. The G+C content of the genomic DNA was 60 mol%. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain CSE-5610T from the two closely related strains. Hence, CSE-5610T represents a novel species of the genus Cohnella, for which we propose the name Cohnella rhizosphaerae sp. nov., with CSE-5610T (=LMG 28080T=CIP 110695T) as the type strain.