Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov., isolated from soil and faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau

Two novel strain pairs (HM61T/HM23 and S-34T/S-58) were isolated from soil and the faeces of Tibetan antelope (Pantholops hodgsonii) collected at the Qinghai-Tibet Plateau of PR China. All four new isolates were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, and short rod-shaped bacteria. The results of phylogenetic analysis based on the full-length 16S rRNA genes and 283 core genomic genes indicated that the four strains were separated into two independent branches belonging to the genus Nocardioides. Strains HM61T and HM23 were most closely related to Nocardioides pelophilus THG T63T (98.58 and 98.65 % 16S rRNA gene sequence similarity). Strains S-34T and S-58 were most closely related to Nocardioides okcheonensis MMS20-HV4-12T (98.89 and 98.89 % 16S rRNA gene sequence similarity). The G+C contents of the genomic DNA of strains HM61T and S-34T were 70.6 and 72.5 mol%, respectively. Strains HM61T, S-34T and the type strains of closely related species in the analysis had average nucleotide identity values of 75.4-90.5 % as well as digital DNA-DNA hybridization values between 20.1 and 40.8 %, which clearly indicated that the four isolates represent two novel species within the genus Nocardioides. The chemotaxonomic characteristics of strains HM61T and S-34T were consistent with the genus Nocardioides. The major fatty acids of all four strains were iso-C16 : 0, C17 : 1  ω8c or C18 : 1  ω9c. For strains HM61T and S-34T, MK-8(H4) was the predominant respiratory quinone, ll-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan, and the polar lipids profiles were composed of diphosphatidylglycerol and phosphatidylglycerol. Based on phylogenetic, phenotypic, and chemotaxonomic data, we propose that strains HM61T and S-34T represent two novel species of the genus Nocardioides, respectively, with the names Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov. The type strains are HM61T (=GDMCC 4.343T=JCM 36399T) and S-34T (=CGMCC 4.7664T=JCM 33792T).

Nocardioides nematodiphilus sp. nov., isolated from rhizosphere of Arabidopsis thaliana

An actinobacterial strain, designated R-N-C8T, was isolated from the rhizosphere soil of Arabidopsis thaliana collected in Yunnan Province, south-west China. Based on the results of 16S rRNA gene sequence analysis, strain R-N-C8T had highest similarity to Nocardioides terrae CGMCC 1.7056T (96.5%), Nocardioides opuntiae KCTC 19804T (96.3%) and Nocardioides currus IB-3T (96.1%), and lower than 96.0 % similarity to other members of the genus Nocardioides . Phylogenetic trees based on 16S rRNA gene sequences indicated that strain R-N-C8T formed an isolated branch with N. terrae CGMCC 1.7056T and N. opuntiae KCTC 19804T. The polar lipids contained phosphatidylglycerol, diphosphatidylglycerol, one unidentified phosphoglycolipid and four unidentified phospholipids in the cellular membrane. The major fatty acids were identified as iso-C16 : 0, anteiso-C17 : 0, iso-C17 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl) and iso-C15 : 0. The predominant respiratory quinone was MK-8(H4) and ll-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The genomic DNA G+C content was 70.9 mol%. The orthologous average nucleotide identiy values between N. terrae CGMCC 1.7056T, N. currus IB-3T and strain R-N-C8T were 77.1 and 75.1 %, respectively. DNA–DNA hybridization values between N. terrae CGMCC 1.7056T, N. currus IB-3T and strain R-N-C8T were 20.7 and 19.9 % respectively. Data from phenotypic and genotypic analyses supported that strain R-N-C8T represents a new species of Nocardioides , for which the name Nocardioides nematodiphilus sp. nov. is proposed. The type strain is R-N-C8T (=CGMCC 1.18723T= KCTC 49528T).

Nocardioides humilatus sp. nov., isolated from farmland soil in the Republic of Korea

A Gram-stain positive, aerobic, irregularly rod-shaped, non-spore-forming bacterium, designated as BN130099T, was isolated from farmland soil sampled in Goesan-gun, Chungbuk, Republic of Korea. Phylogenetic analysis of its 16S rRNA gene sequence showed that the strain is closely related to Nocardioides pelophilus KACC 19192T with 98.11 % similarity. The DNA G+C content of strain BN130099T was 68.84 mol% (draft genome sequence). The genome sequence of BN130099T displayed key enzymes involved in bioremediation of organic pollutants and biosynthetic clusters of saquayamycin. The strain contained ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan and MK-8(H4) as the major respiratory quinone. The predominant fatty acid was iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. The results of physiological and biochemical characterization allowed the phenotypic differentiation of strain BN130099T from N. pelophilus KACC 19192T. The strain represents a novel species of the genus Nocardioides , for which we propose the name Nocardioides humilatus sp. nov. The type strain is BN130099T (=KCTC 49079T=CCTCC AB 2018135T).

Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) and leaves of dandelion (Taraxacum officinale), respectively, on the Qinghai-Tibet Plateau

In the present study, four bacterial strains, two (S-713^T and 406) isolated from faecal samples of Tibetan antelopes and the other two (S-531^T and 1598) from leaves of dandelion collected on the Qinghai-Tibet Plateau of PR China, were analysed using a polyphasic approach. All four isolates were aerobic, rod-shaped, non-motile, oxidase-negative, Gram-stain-positive and catalase-positive. According to four phylogenetic trees, strain pairs S-713^T/406 and S-531^T/1598 form two independent branches belonging to the genus Nocardioides, and are closest to Nocardioides lianchengensis, Nocardioides dokdonensis, Nocardioides salarius, Nocardioides marinisabuli, Nocardioides psychrotolerans and Nocardioides szechwanensis. Although sharing MK8-(H₄) as their major isoprenoid quinone, strains S-713^T and S-531^T contained C_18 : 1  ω9c (24.64 and 16.34 %) and iso-C_16 : 0 (9.74 and 29.38 %), respectively, as their main fatty acids, with remarkable differences in their biochemical profiles but only slight ones in their optimal growth conditions. The chromosomes of strains S-713^T and S-531^T were 4 207 844 bp (G+C content, 73.0 mol%) and 4 809 817 bp (G+C content, 72.5 mol%), respectively. Collectively, the two strain pairs represent two separate novel species of the genus Nocardioides, for which the names Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov. are proposed, with S-713^T (=JCM 33698^T=CGMCC 4.7660^T) and S-531^T (=JCM 33468^T=CGMCC 4.7659^T) as the respective type strains.

Nocardioides stalactiti sp. nov., isolated from a cave stalactite surface

An aerobic, rod-shaped, Gram-stain-positive, actinobacterial strain, designated 1.0914^T, was isolated from a stalactite sample collected from a cave located in Guizhou Province, southwest PR China. Based on 16S rRNA gene sequence analysis, strain 1.0914^T shared highest similarities values with Nocardioides pelophilus CGMCC 4.7388^T (97.7 %), Nocardioides immobilis CCTCC AB 2017083^T (97.5 %) and Nocardioides silvaticus CCTCC AB 2018079^T (97.3 %) and values lower than 97.0 % to other members of the genus Nocardioides. Phylogenetic trees based on 16S rRNA gene sequences indicated that strain 1.0914^T formed an isolated branch with N. pelophilus CGMCC 4.7388^T, N. immobilis CCTCC AB 2017083^T and N. silvaticus CCTCC AB 2018079^T. The polar lipids contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and one unidentified phospholipid in the cellular membrane. The major fatty acids were identified as iso-C_16 : 0, C_18 : 1 ω9c, C_17 : 1 ω8c and C_16 : 0. The predominant respiratory quinone was MK-8(H₄) and ll-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The genomic DNA G+C content was 71.1 mol%. The orthologous average nucleotide identiy values between N. pelophilus CGMCC 4.7388^T, N. immobilis CCTCC AB 2017083^T, N. silvaticus CCTCC 2018079^T and strain 1.0914^T were 82.3, 81.7 and 81.9 % respectively. DNA-DNA hybridization values between N. pelophilus CGMCC 4.7388^T, N. immobilis CCTCC AB 2017083^T, N. silvaticus CCTCC 2018079^T and strain 1.0914^T were 25.2, 24.6 and 24.5 % respectively. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of strain 1.0914^T as representing a new species of Nocardioides, for which the name Nocardioides stalactiti sp. nov. is proposed. The type strain is 1.0914^T (=CCTCC AB 2018266^T=KCTC 49243^T).

Nocardioides antri sp. nov., Isolated from Soil in a Rock Cave

A Gram-positive, aerobic, rod-shaped, non-spore-forming bacterium, designated as BN140041^T, was isolated from cave soil at Gubyeongsan Mountain, Boeun-gun, Chungbuk province in Republic of Korea. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is closely related to Nocardioides silvaticus S-34 ^T, N. pelophilus THG-T63^T, and N. immobilis FLL521^T with 97.4%, 97.1%, and 96.8% similarity. The draft genome length was 4.27 Mb containing 424 contigs with a DNA G + C content of 70.5 mol%. The ANI value between strain BN140044^T and its closely related species N. silvaticus S-34 ^T was 82.6%. The genome sequence of BN140041^T displayed a key enzyme involved in the bioremediation of organic pollutants. The diagnostic diamino acid of peptidoglycan was LL-2,6-diaminopimelic acid. The major respiratory quinone was MK-8(H4), and the major fatty acids (> 5% of the total fatty acids) were iso-C_16:0 (55.3%), C_18:1ω9c (7.7%) and iso-C_17:0 (5.7%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and phosphatidylinositol. The results of genotypical, physiological, and biochemical characterization allow the phenotypic differentiation of strain BN140041^T from related the Nocardioides strains. Therefore, strain BN140041^T represents a novel species of the genus Nocardioides, for which we propose the name Nocardioides antri sp. nov. The type strain is BN140041^T (= KCTC 49080 ^T = CCTCC AB 2018226 ^T).

Kin bias and male pair-bond status shape male-male relationships in a multilevel primate society

Abstract

Male-male social relationships in group-living mammals vary from fierce competition to the formation of opportunistic coalitions or the development of long-lasting bonds. We investigated male-male relationships in Guinea baboons (Papio papio), a species characterized by male-male tolerance and affiliation. Guinea baboons live in a multi-level society, with units of one reproductively active “primary” male, 1–6 females, and offspring at the core level. Together with “bachelor” males, several units form a party, and 2–3 parties constitute a gang. We aimed to clarify to which degree male relationship patterns varied with relatedness and pair-bond status, i.e., whether males had primary or bachelor status. Data were collected from 24 males in two parties of Guinea baboons near Simenti in the Niokolo-Koba National Park in Senegal. Males maintained differentiated and equitable affiliative relationships (“strong bonds”) with other males that were stable over a 4-year period, irrespective of their pair-bond status. Remarkably, most bachelor males maintained strong bonds with multiple primary males, indicating that bachelor males play an important role in the cohesion of the parties. A clear male dominance hierarchy could not be established due to the high degree of uncertainty in individual rank scores, yet bachelor males were more likely to be found at the low end of the dominance hierarchy. Average relatedness was significantly higher between strongly bonded males, suggesting that kin biases contribute to the social preferences of males. Long-term data will be needed to test how male bonds affect male tenure and ultimately reproductive success.

Significance statement

Males living in social groups may employ different strategies to increase their reproductive success, from fierce fighting to opportunistic alliance formation or the development of long-term bonds. To shed light on the factors that shape male strategies, we investigated male-male social relationships in the multilevel society of Guinea baboons (Papio papio) where “primary” males are associated with a small number of females and their offspring in “units” while other males are “bachelors.” Strong bonds occurred among and between primary and bachelor males and strongly bonded males were, on average, more closely related. Bachelor males typically had multiple bond partners and thus play an important role in the fabric of Guinea baboon societies. Across primate species, neither dispersal patterns nor social organization clearly map onto the presence of strong bonds in males, suggesting multiple routes to the evolution of male bonds.

Metagenomic analysis of the dust particles collected from the suction tube and the suction funnel of a dermatological laser smoke evacuator system

In the last few decades, there has essentially been an explosion in the use of lasers in medicine, especially in the area of cosmetic dermatology. Potentially harmful substances are liberated when tissues are vaporized with laser. This creates numerous risks, including the spread of infectious disease. Smoke evacuators are devices that capture and filter laser plume, thereby maintaining a safe environment for the surgical team and patient. Our aim was to characterize the microbial community structure within the suction tube and funnel of the smoke evacuator system, identify their origin, and evaluate pathogenicity. Dust particles were collected from the instruments with a cotton swab. DNA was extracted from the swabs and the transport media, and sequencing was performed using the Illumina HiSeq Xplatform. Metagenomic analysis was conducted using the Empowering the Development of Genomics Expertise (EDGE) Bioinformatics pipeline and custom Python scripts. The most abundant bacterial species were Micrococcus luteus and Brevibacterium casei in the suction tube, and Dermacoccus sp. Ellin 185 and Janibacter hoylei in the suction funnel. A total of 15 medium- to high-quality metagenome-assembled genomes (MAGs) were constructed where we found 104 antibiotic-resistant genes (ARGs) and 741 virulence factors. Findings indicate that the suction tube and funnel are likely a reservoir of virulence factor genes and ARGs, which can possibly be passed on to other bacteria via horizontal gene transfer. We would like to emphasize the health risk these microorganisms pose and the need to reevaluate the current hygiene standards with regard to the smoke evacuator system.

Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil

A Gram-stain-positive, aerobic, non-motile, rod-shaped actinobacterium, designated strain 21Sc5-5^T, was isolated from a soil sample collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, PR China and investigated by using a polyphasic approach. Strain 21Sc5-5^T grew at 10-37 °C (optimum, 28-30 °C), pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-3 % (w/v) NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain 21Sc5-5^T formed a distinct lineage within the genus Nocardioides and had the highest similarity to Nocardioides albidus THG-S11.7^T (97.30 %), followed by Nocardioides kongjuensis A2-4^T (97.22 %), Nocardioides nitrophenolicus NSP 41^T (97.15 %) and Nocardioides caeni MN8^T (97.15 %). The results of chemotaxonomic analyses showed that the isolate possessed ll-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan and MK-8(H₄) as the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and three unidentified lipids. The major fatty acids were iso-C_16 : 0 and 10-methyl C_18 : 0. The genome length of strain 21Sc5-5^T was 4.67 Mb containing 372 contigs and with a DNA G+C content of 70.4 mol%. On the basis of data from phylogenetic, phenotypic and chemotaxonomic analyses, strain 21Sc5-5^T represents a novel species of the genus Nocardioides, for which the name Nocardioides vastitatis sp. nov. is proposed. The type strain is 21Sc5-5^T (=JCM 33365^T=CGMCC 4.7608^T).

Nocardioides speluncae sp. nov., a novel actinobacterium isolated from a karstic subterranean environment sample

A novel actinobacterial strain, designated YIM ART13^T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, South western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were found to aerobic and Gram-stain positive. On the basis of 16S rRNA gene sequence analysis, strain YIM ART13^T was found to be closely related to Nocardioides pakistanensis NCCP 1340^T (96.1% sequence similarity) and is therefore considered to represent a member of the genus Nocardioides. In addition, LL-diaminopimelic acid was identified as the diagnostic diamino acid in the cell wall peptidoglycan. The whole cell sugars were found to be mannose, galactose, glucose and ribose. The major isoprenoid quinone was identified as MK-8(H₄), while the major fatty acids (> 10%) were identified as iso-C_16:0, C_18:1ω9c and C_18:0 10-methyl. The polar lipids were found to contain diphosphatidylglycerol, phosphatidylglycerol phosphatidylinositol and phosphatidylinositol mannoside, an unidentified phospholipid. The genomic DNA G+C content of strain YIM ART13^T was determined from the draft genome sequence to be 70.1 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain YIM ART13^T represents a novel species of the genus Nocardioides, for which the name Nocardioides speluncae sp. nov. is proposed. The type strain is YIM ART13^T (= KCTC 39593^T = DSM 100493^T).