Nocardiopsis deserti sp. nov., isolated from a high altitude Atacama Desert soil

The taxonomic status of a Nocardiopsis strain, designated H13T, isolated from a high altitude Atacama Desert soil, was established by using a polyphasic approach. The strain was found to have chemotaxonomic, cultural and morphological characteristics consistent with its classification within the genus Nocardiopsis and formed a well-supported clade in the Nocardiopsis phylogenomic tree together with the type strains of Nocardiopsis alborubida, Nocardiopsis dassonvillei and Nocardiopsis synnematoformans. Strain H13T was distinguished from its closest relatives by low average nucleotide identity (93.2–94.9 %) and in silico DNA–DNA hybridization (52.5–62.4 %) values calculated from draft genome assemblies and by a range of phenotypic properties. On the basis of these results, it is proposed that the isolate be assigned to the genus Nocardiopsis as Nocardiopsis deserti sp. nov. with isolate H13T (=CGMCC 4.7585T=KCTC 49249T) as the type strai

Culturable endophytic bacteria associated with medicinal plant : molecular phylogeny, distribution and screening for industrially important traits

Inom hälso- och sjukvården ställs idag höga krav på renlighet för att förebygga vårdrelaterade infektioner. Detta gäller inte minst vårdpersonalens händer. Syftet med studien var att undersöka benägenheten att följa de i Handbok för hälso- och sjukvård beskrivna riktlinjerna kring handhygien bland olika yrkeskategorier på en kirurgisk vårdavdelning. Datainsamling skedde genom observationer av under-sköterskor, sjuksköterskor och läkare på den utvalda vårdavdelningen. Studien hade både kvalitativ och kvantitativ ansats. Resultatet visar att avvikelser från handhygienriktlinjerna förekommer i formerna Bristande handhygien, Kontamine-ring, Accessoarer som försvårar effektiv handdesinfektion samt Avsaknad av handskar. Avvikelser från riktlinjerna förekom hos samtliga undersökta yrkeska-tegorier, både före och efter patientkontakt.Palm, B & Stamer, B. Hands – clean tools in nursing. An observational study of the hand hygiene in a surgical ward. Degree project 10 Credit Points. Nursing Programme, Malmö University: Health and Society, Department of Nursing, 2007.In healthcare environments today, cleanliness when it comes to preventing cross infections is in high demand. Not least does this apply to the hands of the health-care workers. The aim of this study was to examine the healthcare workers’ com-pliance to hand hygiene guidelines in a surgical ward. The collection of data was made by observing nurses of all grades and doctors in the chosen ward. The analysis in the study was of both qualitative and quantitative nature. The results show that healthcare workers deviate from hand hygiene guidelines in ways of Insufficient hand hygiene, Contamination, Accessories obstructing effective hand decontamination and Lack of gloves. Deviations from guidelines were found within all three disciplines both before and after interaction with patients.Keywords: Disinfection, contamination, cross infections, hand hygiene, nursing, healthcare workers, observations

Microbial Dark Matter Coming to Light: Challenges and Opportunities

Microbes are the most abundant and diverse cellular life forms on Earth and colonize a wide range of environmental niches. However, more than 99% of bacterial and archaeal species have not been obtained in pure culture [1] and we have only glimpsed the surface of this mysterious microbial world. This is so-called Microbial Dark Matter (MDM): the enormous diversity of yet-uncultivated microbes that microbiologists can only study by using cultivation-independent techniques. Recently, a number of international projects have dramatically increased our understanding of the extent and distribution of microbial diversity, including the Global Catalogue of Microorganisms (GCM), the Genomic Encyclopedia of Bacteria and Archaea (GEBA), the Earth Microbiome Project (EMP), the Genomic Encyclopedia of Bacteria and Archaea-Microbial Dark Matter (GEBA-MDM) and several primate microbiome projects; however, the functional diversity of MDM is still mysterious. This perspective addresses why MDM deserves scientific effort and illustrates challenges and opportunities in the future study of these enigmas

Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments

BackgroundThe Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood.ResultsWe report the isolation of the second member of Atribacterota, Thermatribacter velox gen. nov., sp. nov., within a new family Thermatribacteraceae fam. nov., and the short-term laboratory cultivation of a member of the JS1 lineage, Phoenicimicrobium oleiphilum HX-OS.bin.34TS, both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that Thermatribacter velox B11T and Phoenicimicrobium oleiphilum HX-OS.bin.34TS ferment sugars and n-alkanes, respectively, producing H2, CO2, and acetate as common products. Comparative genomics showed that all members of the Atribacterota lack a complete Wood-Ljungdahl Pathway (WLP), but that the Reductive Glycine Pathway (RGP) is widespread, indicating that the RGP, rather than WLP, is a central hub in Atribacterota metabolism. Ancestral character state reconstructions and phylogenetic analyses showed that key genes encoding the RGP (fdhA, fhs, folD, glyA, gcvT, gcvPAB, pdhD) and other central functions were gained independently in the two classes, Atribacteria (OP9) and Phoenicimicrobiia (JS1), after which they were inherited vertically; these genes included fumarate-adding enzymes (faeA; Phoenicimicrobiia only), the CODH/ACS complex (acsABCDE), and diverse hydrogenases (NiFe group 3b, 4b and FeFe group A3, C). Finally, we present genome-resolved community metabolic models showing the central roles of Atribacteria (OP9) and Phoenicimicrobiia (JS1) in acetate- and hydrocarbon-rich environments.ConclusionOur findings expand the knowledge of the diversity, physiology, ecology, and evolution of the phylum Atribacterota. This study is a starting point for promoting more incisive studies of their syntrophic biology and may guide the rational design of strategies to cultivate them in the laboratory. Video Abstract

Update on the classification of higher ranks in the phylum Actinobacteria

Genome analysis is one of the main criteria for description of new taxa. Availability of genome sequences for all the actinobacteria with a valid nomenclature will, however, require another decade’s works of sequencing. This paper describes the rearrangement of the higher taxonomic ranks of the members of the phylum ‘Actinobacteria’, using the phylogeny of 16S rRNA gene sequences and supported by the phylogeny of the available genome sequences. Based on the refined phylogeny of the 16S rRNA gene sequences, we could arrange all the members of the 425 genera of the phylum ‘Actinobacteria’ with validly published names currently in use into six classes, 46 orders and 79 families, including 16 new orders and 10 new families. The order Micrococcales Prévot 1940 (Approved Lists 1980) emend. Nouioui et al. 2018 is now split into 11 monophyletic orders: the emended order Micrococcales and ten proposed new orders Aquipuribacterales, Beutenbergiales, Bogoriellales, Brevibacteriales, Cellulomonadales, Demequinales, Dermabacterales, Dermatophilales, Microbacteriales and Ruaniales. Further, the class ‘Actinobacteria’ Stackebrandt et al. 1997 emend. Nouioui et al. 2018 was described without any nomenclature type, and therefore the name ‘Actinobacteria’ is deemed illegitimate. In accordance to Rule 8 of the International Code of Nomenclature of Prokaryotes, Parker et al. 2019, we proposed the name Actinomycetia which is formed by using the stem of the name Actinomycetales Buchanan 1917 (Approved Lists 1980) emend. Zhi et al. 2009, to replace the name ‘Actinobacteria’. The nomenclature type of the proposed new class Actinomycetia is the order Actinomycetales Buchanan 1917 (Approved Lists 1980) emend. Zhi et al. 200

Nocardiopsis halophila Al-Tai and Ruan 1994

EMENDED DESCRIPTION OF THE NOCARDIOPSIS HALOPHILA AL-TAI AND RUAN 1994 The description is based on Al-Tai and Ruan [9], Li et al. [3] and Nouioui et al. [10]. Utilization of inositol, raffinose and xylose are variable. Urea hydrolysis is variable. The major phospholipids may contain phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside or phosphatidylmethylethanolamine, besides diphosphotidylglycerol and phosphotidylcholine. May tolerate temperature as high as 50 Ǫ C. The type strain of Nocardiopsis halophila is IQ-H3 T (=CGMCC 4.1195 T = DSM 44494 T =JCM 9892 T). The former type strain of Nocardiopsis baichengensis YIM 90130 T (=CCTCC AA 2040016 T = DSM 44845 T =KCTC 19009 T) is another strain of Nocardiopsis halophila. The G +C content of the type strain is 73.6 mol%.Published as part of Zhang, Xiao-Tong, Salam, Nimaichand, Xiao, Min, Asem, Mipeshwaree Devi & Li, Wen-Jun, 2020, Genome analysis reveals that Nocardiopsis baichengensis Li et al. 2006 is a later heterotypic synonym of Nocardiopsis halophila Al-Tai and Ruan 1994, pp. 89-92 in International Journal of Systematic and Evolutionary Microbiology 70 (1) on page 92, DOI: 10.1099/ijsem.0.003721, http://zenodo.org/record/604867

Biocontrol and plant growth promoting activities of a Streptomyces corchorusii strain UCR3-16 and preparation of powder formulation for application as biofertilizer agents for rice plant

Streptomyces corchorusii strain UCR3-16, obtained from rice rhizospheric soils showed antifungal activities against 6 major rice fungal pathogens by diffusible and volatile compounds production. The strain was found positive for production of fungal cell wall degrading enzymes such as chitinase, beta-1,3-glucanase, beta-1,4-glucanase, lipase and protease. The strain was also positive for plant growth promoting traits. It produced up to 30.5 mu g/ml of IAA and solubilized a significant amount of inorganic phosphate (up to 102 mu g/ml). It also produced 69% siderophore units. The strain also produced ammonia and gave positive result for ACC deaminase activity. Highest vigor index of inoculated seedlings was observed when rice seeds were treated with cell suspension of UCR3-16 corresponding to 4.5 x 10(8) cfu/ml. Bioinoculant-treated seeds also showed similar results under pathogen challenged conditions. In pot trial experiments, UCR3-16-treated rice plants showed significantly increased growth and grain yield production. Powder formulation of the strain was developed using talcum and corn starch as carriers and the shelf-lives were monitored. Talcum formulation showed higher cell-count than corn starch even after 6 months of storage, and optimum condition for storage of the powder formulation were found to be at 4 degrees C. Pot trial experiments using talcum powder formulation also showed significant positive effects on growth of rice plants. Field trial using talcum powder formulation also exhibited significant enhancement in shoot length and weight of shoot and root, and total grain yield and weight of grains in rice plants. Talcum formulation also significantly reduced the sheath blight disease in rice leaves. (C) 2016 Published by Elsevier GmbH

Acidotolerant Streptomyces sp. MBRL 10 from limestone quarry site showing antagonism against fungal pathogens and growth promotion in rice plants

Acidotolerant Streptomyces sp. MBRL 10 isolated from limestone deposit site on Gauze’s medium No. 1 (pH 5.3) showed significant antagonism against the tested fungal pathogens. It exhibited the highest mycelial growth inhibition by diffusible and volatile compound(s) production against Rhizoctonia solani. Culture filtrates also exhibited significant inhibition zone but the inhibition activities vanished when sterilized. The strain produced chitinase, β-1,3-glucanase, lipase, protease and ammonia but not β-1,4-glucanase. It could produce 25 μg/ml of indole acetic acid, solubilize up to 140 μg/ml of phosphate with a concomitant decrease in pH of the medium. The bioactive actinomycete strain produced hydroxamate type of siderophore. Casamino acid was found to be the best medium for siderophore production (87% siderophore units).MBRL 10 showed the highest rice seedlings vigor index corresponding to an inoculum size of 0.3 × 108 cfu/ml. Strain treated rice seeds at an inoculum size of 0.3 × 108 cfu/ml showed higher germination percentage and significantly enhanced (P ⩽ 0.05) the growth of seedlings. Strain treated rice seedlings challenged with pathogens also exhibited higher germination percentages and significantly enhanced (P ⩽ 0.05) growth over seedlings challenged with pathogen alone in the absence of the bioinoculant. Rice plants treated with the strain significantly promote (P ⩽ 0.05) the growth under nethouse conditions. Keywords: Streptomyces sp. MBRL 10, Acidotolerant, Antagonism, Plant growth promoting traits, Vigor index, Rice plant

Streptomyces manipurensis MBRL 201T as potential candidate for biocontrol and plant growth promoting agent for rice

741-749Globally, there is a need to enhance agricultural productivity safely to feed the growing human population without massive use of chemical pesticides and fertilizers, as it causes adverse effects on environment. Biocontrol activities and use of plant growth promoting (PGP) bacteria holds great promise for an ecofriendly sustainable organic agriculture. In this context, here, we studied a novel species, Streptomyces manipurensis MBRL 201T for its biocontrol and growth promoting potential in rice. It was found to exhibit antagonistic activity against 6 important rice fungal pathogens by diffusible and volatile compounds production. The culture filtrates also exhibited significant inhibition. The strain was positive for PKS-II and NRPS genes. The strain produced fungal cell wall degrading enzymes, such as chitinase, β-1,4-glucanase, lipase and protease, and volatile compound, such as ammonia. The strain could produce 50.05 µg mL-1 of IAA, highest siderophore in starch casein nitrate broth (88.05%) and solubilize 76 µg mL-1 of phosphate. The strain was also positive for ACC deaminase activity. Highest vigor index was observed when rice seeds were treated with 6×107cfu mL-1 of MBRL 201T. The strain could enhance seeds germination and growth of rice seedlings even under pathogen challenged conditions. Treatment of the strain through seeds dipping and foliar spray exhibited significant effects on growth of rice under greenhouse and field conditions. The strain has the potential to be used as biocontrol and/ biofertilizing agents for application in rice plant

Acidotolerant Streptomyces sp. MBRL 10 from limestone quarry site showing antagonism against fungal pathogens and growth promotion in rice plants

AbstractAcidotolerant Streptomyces sp. MBRL 10 isolated from limestone deposit site on Gauze’s medium No. 1 (pH 5.3) showed significant antagonism against the tested fungal pathogens. It exhibited the highest mycelial growth inhibition by diffusible and volatile compound(s) production against Rhizoctonia solani. Culture filtrates also exhibited significant inhibition zone but the inhibition activities vanished when sterilized. The strain produced chitinase, β-1,3-glucanase, lipase, protease and ammonia but not β-1,4-glucanase. It could produce 25μg/ml of indole acetic acid, solubilize up to 140μg/ml of phosphate with a concomitant decrease in pH of the medium. The bioactive actinomycete strain produced hydroxamate type of siderophore. Casamino acid was found to be the best medium for siderophore production (87% siderophore units).MBRL 10 showed the highest rice seedlings vigor index corresponding to an inoculum size of 0.3×108cfu/ml. Strain treated rice seeds at an inoculum size of 0.3×108cfu/ml showed higher germination percentage and significantly enhanced (P⩽0.05) the growth of seedlings. Strain treated rice seedlings challenged with pathogens also exhibited higher germination percentages and significantly enhanced (P⩽0.05) growth over seedlings challenged with pathogen alone in the absence of the bioinoculant. Rice plants treated with the strain significantly promote (P⩽0.05) the growth under nethouse conditions