Cohnella plantaginis sp. nov., a novel nitrogen-fixing species isolated from plantain rhizosphere soil

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.

The Soil Microbiome of the Laurel Forest in Garajonay National Park (La Gomera, Canary Islands): Comparing Unburned and Burned Habitats after a Wildfire

The evergreen laurel forest is a relic of ancient subtropical/tropical forests, of which the best remnant in the Canary Islands is in Garajonay National Park, on La Gomera island. The soil microbiome associated with a mature undisturbed (unburned) laurel forest was characterized at two locations at different topographical positions on the mountain: The slope and the ridge crest. Given the unusual circumstance of an intense wildfire that severely affected part of this forest, the burned soils were also studied. The soil in undisturbed areas was relatively uniform. The bacterial community composition was dominated by bacteria from phyla Proteobacteria, Acidobacteria, and Actinobacteria. The wildfire changed the composition of the bacterial communities. The Acidobacteria, Actinobacteria, and Alphaproteobacteria (dominant class in unburned forests) significantly decreased in burned soils along with a parallel high increase in Betaproteobacteria, Bacteroidetes, and Firmicutes. We further showed the dramatic effect of a wildfire on the soil microbiome of the laurel forest, appearing as a loss of species richness and diversity, species dominance, and changes in the composition of the bacterial communities.

Variation in rhizosphere microbiota correlates with edaphic factor in an abandoned antimony tailing dump

The distribution pattern of root-associated bacteria in native plant growth in tailing dumps with extreme conditions remains poorly understood and largely unexplored. Herein we chose a native plant, Bidens bipinnata, growing on both an Sb tailing dump (WKA) and adjacent normal soils (WKC) to in-depth understand the distribution pattern of root-associated bacteria and their responses on environmental factors. We found that the rhizosphere microbial diversity indices in the tailing dump were significantly different from that in the adjacent soil, and that such variation was significantly related with soil nutrients (TC, TOC, TN) and metal(loid) concentrations (Sb and As). Some dominant genera were significant enriched in WKA, suggesting their adaption to harsh environments. Notably, these genera are proposed to be involved in nutrient and metal(liod) cycling, such as nitrogen fixing (Devosia, Cellvibrio, Lysobacter, and Cohnella), P solubilizing (Flavobacterium), and Sb and As oxidation (Paenibacillus, Bacillus, Pseudomonas, and Thiobacillus). Our results suggest that certain root-associated bacteria in tailing dump were governed by soil edaphic factors and play important ecological roles in nutrient amendments and metal cycling for the successful colonization of Bidens bipinnata in this tailing dump.

Cohnella kolymensis sp. nov., a novel bacillus isolated from Siberian permafrost

A facultative anaerobic, rod-shaped, endospore-forming and non-motile bacterium was isolated from permafrost sediment cores in the Kolyma lowland, Siberia, Russia. The permafrost isolate clustered with members of the genus Cohnella on the basis of 16S rRNA gene sequence analysis and showed the highest sequence similarity to Cohnella saccharovorans CJ22^T (96.3 %), followed by Cohnella cellulosilytica FCN3-3^T (96.0 %) and Cohnella panacarvi KCTC 13060^T (96.0 %). The chemotaxonomic characteristics (quinone system, cellular fatty acids and polar lipid profile) of strain 20.16^T were consistent with members of the genus Cohnella. The peptidoglycan diaminoacids included meso-diaminopimelic acid and a small amount of ll-diaminopimelic acid. The molar ratio and composition of major amino acids (meso-diaminopimelic acid, alanine, and glutamic acid) correspond to the peptydoglycan type A1γ. The estimated genome size of strain 20.16^T is 4.34 Mb (lower than those in other Cohnella species). The genome has a G+C content of 50.5 mol% and encodes 4843 predicted genes, of these 4740 are protein-coding ones. The results of chemotaxonomic, physiological and biochemical characterization allowed clear differentiation of strain 20.16^T from the closest Cohnella species. Based on data provided, a new species Cohnella kolymensis sp. nov. is proposed, with 20.16^T (=VKM B-2846^T=DSM 104983^T) as the type strain.

Bacteria utilizing plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil

Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, ¹³ C-CO₂ labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in ¹³ C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in ¹³ C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear ¹³ C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.

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).

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.