Molecular identification of genus Pipistrellus (Mammalia: Chiroptera) from Fata region, Pakistan

A total of 10 specimens were captured from selected sites of Bajaur Agency FATA, Pakistan using mist nets. The captured specimens were morphologically identified and various morphometric measurements were taken. The head and Body length (HB) of Pipistrellus coromondra and Pipistrellus kuhlii lepidus (n=10) was 43±0.11 mm and 45±1.1 respectively. Morphologically identified Pipistrellus kuhlii confirmed as Pipistrellus kuhlii lepidus based on 16S rRNA sequences. The DNA sequences were submitted to GenBank and accession numbers were obtained (MN 719478 and MT430902). The available 16S rRNA gene sequences of Pipistrellus coromondra and Pipistrellus kuhlii lepidus were retrieved from NCBI and incorporated in N-J tree analysis. Overall, the interspecific genetic variations among Pipistrellus coromondra and Pipistrellus kuhlii lepidus were 8% and 1% respectively. In our recommendation, a comprehensive molecular identification of bats is need of hour to report more cryptic and new species from Pakistan.

Highly Distinct Microbial Communities in Elevated Strings and Submerged Flarks in the Boreal Aapa-Type Mire

Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. In this paper, we characterized microbial diversity patterns in the surface peat layers of the neighboring string and flark structures located within the mire site in the Vologda region of European North Russia, using 16S rRNA gene sequencing. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks.

Gottfriedia Endophyticus sp. nov., a Novel Indole-Acetic Acid Producing Bacterium Isolated From The Roots of Rice Plant

A Gram-stain-positive, aerobic, motile and rod-shaped bacterium, designated RG28T, was isolated from the roots of rice plant collected from paddy fields in Goyang, South Korea. Cells of the strain were oxidase-negative but catalase-positive. Strain RG28T was found to grow at 10–50°C (optimum, 25–30°C), pH 5.0–10.0 (optimum, pH 7.0) and in 1.0–5.0 % (w/v) NaCl (optimum, 0%). The cell-wall peptidoglycan contained meso-diaminopimelic acid and the predominant menaquinones were MK-7 and MK-6.The predominant cellular fatty acids were C16:0, iso-C15:0 and anteiso-C15:0. The major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, four unidentified aminophosphoglycolipids, four unidentified aminophospholipids, two unidentified glycolipids, one unidentified aminoglycolipid and four unidentified lipids. The genomic DNA G+C content was 33.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was closely related to Gottfriedia acidiceleris CBD 119T (98.6%), Gottfriedia solisilvae LMG 18422T (98.5 %) and Gottfriedia luciferensis LMG 18422T (98.4 %). The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between strain RG28T and type strains of Gottfriedia species were lower than the cut-offs (≥95–96 % for ANI and ≥70 % for isDDH) required to define a bacterial species. Meanwhile, the strain has the ability to produce indole-acetic acid (40.5 µg/mL). Phylogenetic, physiological and chemotaxonomic data suggested that strain RG28T represented a novel species of the genus Gottfriedia, for which the name Gottfriedia endophyticus sp. nov. is proposed, with the type strain RG28T (=KCTC 43327T=TBRC 15151T).Repositories: The draft genome and 16S rRNA gene sequences of strain RG28T have been deposited in GenBank/EMBL/DDBJ under accession numbers JAGIYQ000000000 and MW386408 respectively.

Microvirga Puerhi Sp. Nov., Isolated from Puerh Tea Garden Soil

Strain WGZ8T was isolated from a soil sample of Puerh tea garden in Puer city, Southwest China. The isolate was rod-shaped, Gram-stain negative, aerobic, non-motile. Growth occurred within 0-3.0% (w/v) NaCl (optimal concentration, 0-1.0%), pH 5.0-11.0 (optimal pH, 7.0) and 10-40°C (optimal temperature, 28°C). 16S rRNA gene sequences based phylogenetic and phylogenomic analysis revealed that WGZ8T belonged to the genus Microvirga. Its major cellular fatty acids were C19:0 cyclo ω8c, C16:0, C18:1ω7c and/or C18:1ω6c. The profile of polar lipids included phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and phosphatidyl-glycerol. The only respiratory quinone was detected as ubiquinone 10 (Q-10). The genome size of strain WGZ8T was 5.17MB, and the content of DNA G+C was 61%. Based on the results of digital DNA-DNA hybridization and phenotypic results, strain WGZ8T could be concluded as a novel species of the genus Microvirga, for which the name Microvirga puerhi sp. nov. is proposed. The type strain is WGZ8T (=CGMCC 1.19171T=JCM XXXXT).

Arthrobacter cheniae and Arthrobacter frigidicola sp. nov., isolated from a glacier

Two Gram-stain-positive, aerobic, rod-shaped, pink and light pink colony-forming bacteria, designated as Hz2T and MDT2-14T, respectively, were isolated from glacier cryoconite samples. Comparisons based on 16S rRNA gene sequences showed that strains Hz2T and MDT2-14T take Arthrobacter bussei KR32T and Arthrobacter zhaoguopingii J391T as their closest neighbours, respectively. The average nucleotide identity values between the two novel strains and their closest relatives were 83.56 and 93.06 %, respectively. The two strains contain MK-9(H2) as their predominant menaquinone. The polar lipids of both strains were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The major fatty acids of strain Hz2T were anteiso-C15 : 0, summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C15 : 0, while the major fatty acids of strain MDT2-14T were anteiso-C15 : 0 and anteiso-C17 : 0. Based on these data, we propose two novel species, Arthrobacter cheniae sp. nov. (Hz2T = CGMCC 1.9262T=NBRC 113086T) and Arthrobacter frigidicola sp. nov. (MDT2-14T=CGMCC 1.9882T=NBRC 113089T).

Rhizobium lacunae sp. nov., Isolated From a Freshwater Pond

Bacterial strain designated CSW-27T was isolated from a freshwater pond in Taiwan. Cells were Gram-stain-negative, aerobic, oxidase-positive, catalase-negative, rod-shaped and motile by flagella. Strain CSW-27T grew at 20-40 oC (optimum, 30-37 oC), at pH 5-9 (optimum, pH 6-7) and in the presence of 0-4% NaCl (optimum, 0%). Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set revealed that strain CSW-27T was affiliated with species in the genus Rhizobium. Analysis of 16S rRNA gene sequences showed that strain CSW-27T had the highest similarity to Rhizobium straminoryzae CC-LY845T (98.5%) followed by Rhizobium capsici CC-SKC2T (96.9%). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain CSW-27T and the closely related Rhizobium species were 73.4-86.5, 66.0-88.8 and 13.3-22.1%, respectively. The principal fatty acid was summed feature 8 (C18:1ω7c and/or C18:1ω6c). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, one uncharacterized aminophospholipid, three uncharacterized aminolipids and two uncharacterized lipids. The predominant polyamine was spermidine. The major isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CSW-27T was 63.3%. These polyphasic taxonomic data indicited that strain CSW-27T should be considered as representing a novel species in the genus Rhizobium, for which the name Rhizobium lacunae sp. nov. is proposed with strain CSW-27T (=BCRC 81244T =LMG 31684T) as the type strain.

Isolation and Characterization of Levoglucosan Metabolizing Bacteria

Bacteria were isolated from wastewater and soil containing charred wood remnants based on their ability to use levoglucosan as a sole carbon source and on their levoglucosan dehydrogenase (LGDH) activity. On the basis of their 16S rRNA gene sequences, these bacteria represented diverse genera of Microbacterium, Paenibacillus , Shinella , and Klebsiella . Genomic sequencing of the isolates verified that two isolates represented novel species, Paenibacillus athensensis MEC069 T and Shinella sumterensis MEC087 T , while the remaining isolates were closely related to either Microbacterium lacusdiani or Klebsiella pneumoniae . The genetic sequence of LGDH, lgdA , was found in the genomes of these four isolates as well as Pseudarthrobacter phenanthrenivorans Sphe3. The identity of the P. phenanthrenivorans LGDH was experimentally verified following recombinant expression in E. coli . Comparison of the putative genes surrounding lgdA in the isolate genomes indicated that several other gene products facilitate the bacterial catabolism of levoglucosan, including a putative sugar isomerase and several transport proteins. Importance Levoglucosan is the most prevalent soluble carbohydrate remaining after high temperature pyrolysis of lignocellulosic biomass, but it is not fermented by typical production microbes such as Escherichia coli and Saccharomyces cerevisiae . A few fungi metabolize levoglucosan via the enzyme levoglucosan kinase, while several bacteria metabolize levoglucosan via levoglucosan dehydrogenase. This study describes the isolation and characterization of four bacterial species which degrade levoglucosan. Each isolate is shown to contain several genes within an operon involved in levoglucosan degradation, furthering our understanding of bacteria which metabolize levoglucosan.

Peat-Inhabiting Verrucomicrobia of the Order Methylacidiphilales Do Not Possess Methanotrophic Capabilities

Methanotrophic verrucomicrobia of the order Methylacidiphilales are known as extremely acidophilic, thermophilic or mesophilic bacteria that inhabit acidic geothermal ecosystems. The occurrence of verrucomicrobial methanotrophs in other types of acidic environments remains an open question. Notably, Methylacidiphilales-affiliated 16S rRNA gene sequences are commonly retrieved from acidic (pH 3.5–5.5) peatlands. In this study, we compared the patterns of verrucomicrobial diversity in four acidic raised bogs and six neutral fens located in European North Russia. Methylacidiphilales-like 16S rRNA gene reads displaying 83–86% similarity to 16S rRNA gene sequences of currently described verrucomicrobial methanotrophs were recovered exclusively from raised bogs. Laboratory incubation of peat samples with 10% methane for 3 weeks resulted in the pronounced increase of a relative abundance of alphaproteobacterial methanotrophs, while no response was detected for Methylacidiphilales-affiliated bacteria. Three metagenome-assembled genomes (MAGs) of peat-inhabiting Methylacidiphilales bacteria were reconstructed and examined for the presence of genes encoding methane monooxygenase enzymes and autotrophic carbon fixation pathways. None of these genomic determinants were detected in assembled MAGs. Metabolic reconstructions predicted a heterotrophic metabolism, with a potential to hydrolyze several plant-derived polysaccharides. As suggested by our analysis, peat-inhabiting representatives of the Methylacidiphilales are acidophilic aerobic heterotrophs, which comprise a sister family of the methanotrophic Methylacidiphilaceae.

Agrobacterium leguminum sp. nov., isolated from nodules of Phaseolus vulgaris in Spain

Two endophytic strains, coded MOVP5T and MOPV6, were isolated from nodules of Phaseolus vulgaris plants grown on agricultural soil in Southeastern Spain, and were characterized through a polyphasic taxonomy approach. Their 16S rRNA gene sequences showed 99.3 and 99.4 %, 98.9 and 99.6 %, and 99.0 and 98.7% similarity to ‘ A. deltaense ’ YIC 4121T, A. radiobacter LGM 140T, and A. pusense NRCPB10T, respectively. Multilocus sequence analysis based on sequences of recA and atpD genes suggested that these two strains could represent a new Agrobacterium species with less than 96.5 % similarity to their closest relatives. PCR amplification of the telA gene, involved in synthesis of protelomerase, confirmed the affiliation of strains MOPV5T and MOPV6 to the genus Agrobacterium . Whole genome average nucleotide identity and digital DNA–DNA hybridization average values were less than 95.1 and 66.7 %, respectively, with respect to its closest related species. Major fatty acids in strain MOPV5T were C18 : 1 ω7c/C18 : 1 ω6c in summed feature 8, C19 : 0 cyclo ω8c, C16 : 0 and C16 : 0 3-OH. Colonies were small to medium, pearl-white coloured on YMA at 28 °C and growth was observed at 10–42 °C, pH 5.0–10.0 and with 0.0–0.5 % (w/v) NaCl. The DNA G+C content was 59.9 mol%. These two strains differ from all other genomovars of Agrobacterium found so far, including those that have not yet given a Latin name. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strain MOPV5T as representing a novel species of Agrobacterium , for which the name Agrobacterium leguminum sp. nov. is proposed. The type strain is MOPV5T (=CECT 30096T=LMG 31779T).

New cyanobacterium Aliterella vladivostokensis sp. nov. (Aliterellaceae, Chroococcidiopsidales), isolated from temperate monsoon climate zone (Vladivostok, Russia)

A new coccoid cyanobacterium Aliterella vladivostokensis sp. nov. was described from an urban aerophytic habitat in a temperate monsoon climate (Vladivostok, Russia) using a polyphasic approach. Phylogenetic analyses based on the 16S rRNA gene sequences confirmed that our isolate was a member of the Aliterella genus clade. Aliterella species are hardly distinguishable from each other morphologically and were described from highly contrasting natural and artificial environments with only a few records from several continents. Despite high similarity of morphometric data for A. vladivostokensis and A. antarctica cells and a compensatory base change in the D1–D1′ helix shared by these species; high percent of dissimilarity (11.6±1.3) between their 16S–23S internal transcribed spacer sequences with at least 5 autapomorphic mutations in the D1–D1′ and Box-B helices, and distinct folding patterns of the Box-B helix allowed us to erect a new species.