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  Subjects -> BIOLOGY (Total: 3036 journals)
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BIOLOGY (1440 journals)                  1 2 3 4 5 6 7 8 | Last

Showing 1 - 200 of 1720 Journals sorted alphabetically
AAPS Journal     Hybrid Journal   (Followers: 22)
Achievements in the Life Sciences     Open Access   (Followers: 4)
ACS Synthetic Biology     Full-text available via subscription   (Followers: 24)
Acta Biologica Colombiana     Open Access   (Followers: 7)
Acta Biologica Hungarica     Full-text available via subscription   (Followers: 4)
Acta Biologica Sibirica     Open Access  
Acta Biomaterialia     Hybrid Journal   (Followers: 26)
Acta Biotheoretica     Hybrid Journal   (Followers: 4)
Acta Chiropterologica     Full-text available via subscription   (Followers: 6)
acta ethologica     Hybrid Journal   (Followers: 4)
Acta Limnologica Brasiliensia     Open Access   (Followers: 3)
Acta Médica Costarricense     Open Access   (Followers: 2)
Acta Musei Silesiae, Scientiae Naturales : The Journal of Silesian Museum in Opava     Open Access  
Acta Neurobiologiae Experimentalis     Open Access  
Acta Parasitologica     Hybrid Journal   (Followers: 10)
Acta Scientiarum. Biological Sciences     Open Access   (Followers: 2)
Acta Scientifica Naturalis     Open Access   (Followers: 2)
Actualidades Biológicas     Open Access   (Followers: 1)
Advanced Health Care Technologies     Open Access   (Followers: 4)
Advanced Studies in Biology     Open Access  
Advances in Antiviral Drug Design     Full-text available via subscription   (Followers: 4)
Advances in Bioinformatics     Open Access   (Followers: 20)
Advances in Biological Regulation     Hybrid Journal   (Followers: 4)
Advances in Biosensors and Bioelectronics     Open Access   (Followers: 7)
Advances in Cell Biology     Open Access   (Followers: 25)
Advances in Cellular and Molecular Biology of Membranes and Organelles     Full-text available via subscription   (Followers: 13)
Advances in Developmental Biology     Full-text available via subscription   (Followers: 12)
Advances in DNA Sequence-Specific Agents     Full-text available via subscription   (Followers: 6)
Advances in Ecological Research     Full-text available via subscription   (Followers: 47)
Advances in Environmental Sciences - International Journal of the Bioflux Society     Open Access   (Followers: 21)
Advances in Enzyme Research     Open Access   (Followers: 9)
Advances in Experimental Biology     Full-text available via subscription   (Followers: 9)
Advances in Genome Biology     Full-text available via subscription   (Followers: 11)
Advances in High Energy Physics     Open Access   (Followers: 19)
Advances in Human Biology     Open Access   (Followers: 2)
Advances in Life Science and Technology     Open Access   (Followers: 14)
Advances in Life Sciences     Open Access   (Followers: 6)
Advances in Marine Biology     Full-text available via subscription   (Followers: 16)
Advances in Molecular and Cell Biology     Full-text available via subscription   (Followers: 23)
Advances in Organ Biology     Full-text available via subscription   (Followers: 2)
Advances in Planar Lipid Bilayers and Liposomes     Full-text available via subscription   (Followers: 3)
Advances in Regenerative Biology     Open Access   (Followers: 1)
Advances in Space Biology and Medicine     Full-text available via subscription   (Followers: 5)
Advances in Structural Biology     Full-text available via subscription   (Followers: 8)
Advances in Virus Research     Full-text available via subscription   (Followers: 6)
African Journal of Range & Forage Science     Hybrid Journal   (Followers: 6)
AFRREV STECH : An International Journal of Science and Technology     Open Access   (Followers: 1)
Ageing Research Reviews     Hybrid Journal   (Followers: 9)
Aging Cell     Open Access   (Followers: 11)
Agrokémia és Talajtan     Full-text available via subscription   (Followers: 2)
Agrokreatif Jurnal Ilmiah Pengabdian kepada Masyarakat     Open Access  
AJP Cell Physiology     Full-text available via subscription   (Followers: 14)
AJP Endocrinology and Metabolism     Full-text available via subscription   (Followers: 23)
AJP Lung Cellular and Molecular Physiology     Full-text available via subscription   (Followers: 3)
Al-Kauniyah : Jurnal Biologi     Open Access  
Alasbimn Journal     Open Access   (Followers: 1)
AMB Express     Open Access   (Followers: 1)
Ambix     Hybrid Journal   (Followers: 3)
American Biology Teacher     Full-text available via subscription   (Followers: 13)
American Fern Journal     Full-text available via subscription   (Followers: 1)
American Journal of Agricultural and Biological Sciences     Open Access   (Followers: 10)
American Journal of Bioethics     Hybrid Journal   (Followers: 10)
American Journal of Human Biology     Hybrid Journal   (Followers: 13)
American Journal of Medical and Biological Research     Open Access   (Followers: 8)
American Journal of Plant Sciences     Open Access   (Followers: 18)
American Journal of Primatology     Hybrid Journal   (Followers: 15)
American Malacological Bulletin     Full-text available via subscription   (Followers: 3)
American Naturalist     Full-text available via subscription   (Followers: 74)
Amphibia-Reptilia     Hybrid Journal   (Followers: 6)
Anaerobe     Hybrid Journal   (Followers: 4)
Analytical Methods     Full-text available via subscription   (Followers: 11)
Anatomical Science International     Hybrid Journal   (Followers: 2)
Animal Cells and Systems     Hybrid Journal   (Followers: 4)
Annales de Limnologie - International Journal of Limnology     Hybrid Journal   (Followers: 1)
Annales françaises d'Oto-rhino-laryngologie et de Pathologie Cervico-faciale     Full-text available via subscription   (Followers: 3)
Annales Henri Poincaré     Hybrid Journal   (Followers: 3)
Annales UMCS, Biologia     Open Access   (Followers: 1)
Annals of Applied Biology     Hybrid Journal   (Followers: 7)
Annals of Biomedical Engineering     Hybrid Journal   (Followers: 18)
Annals of Human Biology     Hybrid Journal   (Followers: 4)
Annual Review of Biomedical Engineering     Full-text available via subscription   (Followers: 14)
Annual Review of Biophysics     Full-text available via subscription   (Followers: 24)
Annual Review of Cancer Biology     Full-text available via subscription   (Followers: 1)
Annual Review of Cell and Developmental Biology     Full-text available via subscription   (Followers: 37)
Annual Review of Food Science and Technology     Full-text available via subscription   (Followers: 16)
Annual Review of Genomics and Human Genetics     Full-text available via subscription   (Followers: 22)
Annual Review of Phytopathology     Full-text available via subscription   (Followers: 10)
Anthropological Review     Open Access   (Followers: 24)
Anti-Infective Agents     Hybrid Journal   (Followers: 3)
Antibiotics     Open Access   (Followers: 9)
Antioxidants     Open Access   (Followers: 4)
Antioxidants & Redox Signaling     Hybrid Journal   (Followers: 9)
Antonie van Leeuwenhoek     Hybrid Journal   (Followers: 5)
Anzeiger für Schädlingskunde     Hybrid Journal   (Followers: 1)
Apidologie     Hybrid Journal   (Followers: 4)
Apmis     Hybrid Journal   (Followers: 1)
APOPTOSIS     Hybrid Journal   (Followers: 8)
Applied Bionics and Biomechanics     Open Access   (Followers: 8)
Applied Vegetation Science     Full-text available via subscription   (Followers: 9)
Aquaculture Environment Interactions     Open Access   (Followers: 2)
Aquaculture International     Hybrid Journal   (Followers: 22)
Aquaculture Reports     Open Access   (Followers: 3)
Aquaculture, Aquarium, Conservation & Legislation - International Journal of the Bioflux Society     Open Access   (Followers: 6)
Aquatic Biology     Open Access   (Followers: 5)
Aquatic Ecology     Hybrid Journal   (Followers: 32)
Aquatic Ecosystem Health & Management     Hybrid Journal   (Followers: 14)
Aquatic Science and Technology     Open Access   (Followers: 3)
Aquatic Toxicology     Hybrid Journal   (Followers: 21)
Archaea     Open Access   (Followers: 3)
Archiv für Molluskenkunde: International Journal of Malacology     Full-text available via subscription   (Followers: 3)
Archives of Biomedical Sciences     Open Access   (Followers: 7)
Archives of Microbiology     Hybrid Journal   (Followers: 8)
Archives of Natural History     Hybrid Journal   (Followers: 8)
Archives of Oral Biology     Hybrid Journal   (Followers: 2)
Archives of Virology     Hybrid Journal   (Followers: 5)
Archivum Immunologiae et Therapiae Experimentalis     Hybrid Journal   (Followers: 2)
Arid Ecosystems     Hybrid Journal   (Followers: 3)
Arquivos do Instituto Biológico     Open Access   (Followers: 1)
Arquivos do Museu Dinâmico Interdisciplinar     Open Access  
Arthropod Structure & Development     Hybrid Journal   (Followers: 2)
Arthropods     Open Access   (Followers: 1)
Artificial DNA: PNA & XNA     Hybrid Journal   (Followers: 3)
Artificial Photosynthesis     Open Access   (Followers: 1)
Asian Bioethics Review     Full-text available via subscription   (Followers: 2)
Asian Journal of Biodiversity     Open Access   (Followers: 5)
Asian Journal of Biological Sciences     Open Access   (Followers: 3)
Asian Journal of Cell Biology     Open Access   (Followers: 6)
Asian Journal of Developmental Biology     Open Access   (Followers: 2)
Asian Journal of Medical and Biological Research     Open Access   (Followers: 2)
Asian Journal of Nematology     Open Access   (Followers: 4)
Asian Journal of Poultry Science     Open Access   (Followers: 4)
Australian Life Scientist     Full-text available via subscription   (Followers: 2)
Australian Mammalogy     Hybrid Journal   (Followers: 6)
Autophagy     Hybrid Journal   (Followers: 2)
Avian Biology Research     Full-text available via subscription   (Followers: 5)
Avian Conservation and Ecology     Open Access   (Followers: 13)
Bacteriology Journal     Open Access   (Followers: 2)
Bacteriophage     Full-text available via subscription   (Followers: 4)
Bangladesh Journal of Bioethics     Open Access  
Bangladesh Journal of Plant Taxonomy     Open Access  
Bangladesh Journal of Scientific Research     Open Access   (Followers: 2)
Berita Biologi     Open Access   (Followers: 1)
Between the Species     Open Access   (Followers: 1)
Bio Tribune Magazine     Hybrid Journal  
BIO Web of Conferences     Open Access  
BIO-Complexity     Open Access  
Bio-Grafía. Escritos sobre la Biología y su enseñanza     Open Access  
Bioanalytical Reviews     Hybrid Journal   (Followers: 2)
Biocatalysis and Biotransformation     Hybrid Journal   (Followers: 6)
Biochemistry and Cell Biology     Hybrid Journal   (Followers: 14)
Biochimie     Hybrid Journal   (Followers: 7)
BioControl     Hybrid Journal   (Followers: 5)
Biocontrol Science and Technology     Hybrid Journal   (Followers: 5)
Biodemography and Social Biology     Hybrid Journal   (Followers: 1)
BioDiscovery     Open Access   (Followers: 2)
Biodiversity : Research and Conservation     Open Access   (Followers: 29)
Biodiversity and Natural History     Open Access   (Followers: 6)
Biodiversity Data Journal     Open Access   (Followers: 3)
Biodiversity Informatics     Open Access   (Followers: 1)
Biodiversity Information Science and Standards     Open Access  
Bioedukasi : Jurnal Pendidikan Biologi FKIP UM Metro     Open Access  
Bioeksperimen : Jurnal Penelitian Biologi     Open Access  
Bioelectrochemistry     Hybrid Journal   (Followers: 2)
Bioelectromagnetics     Hybrid Journal   (Followers: 1)
Bioenergy Research     Hybrid Journal   (Followers: 2)
Bioengineering and Bioscience     Open Access   (Followers: 1)
BioEssays     Hybrid Journal   (Followers: 10)
Bioethics     Hybrid Journal   (Followers: 14)
BioéthiqueOnline     Open Access  
Biofabrication     Hybrid Journal   (Followers: 3)
Biogeosciences (BG)     Open Access   (Followers: 10)
Biogeosciences Discussions (BGD)     Open Access   (Followers: 1)
Bioinformatics     Hybrid Journal   (Followers: 285)
Bioinformatics and Biology Insights     Open Access   (Followers: 15)
Bioinspiration & Biomimetics     Hybrid Journal   (Followers: 7)
Biointerphases     Open Access   (Followers: 1)
Biojournal of Science and Technology     Open Access  
Biologia     Hybrid Journal  
Biologia on-line : Revista de divulgació de la Facultat de Biologia     Open Access  
Biological Bulletin     Partially Free   (Followers: 5)
Biological Control     Hybrid Journal   (Followers: 4)
Biological Invasions     Hybrid Journal   (Followers: 17)
Biological Journal of the Linnean Society     Hybrid Journal   (Followers: 18)
Biological Letters     Open Access   (Followers: 5)
Biological Procedures Online     Open Access  
Biological Psychiatry     Hybrid Journal   (Followers: 45)
Biological Psychology     Hybrid Journal   (Followers: 6)
Biological Research     Open Access  
Biological Rhythm Research     Hybrid Journal   (Followers: 2)
Biological Theory     Hybrid Journal   (Followers: 2)
Biological Trace Element Research     Hybrid Journal  
Biologicals     Full-text available via subscription   (Followers: 9)
Biologics: Targets & Therapy     Open Access   (Followers: 1)
Biologie Aujourd'hui     Full-text available via subscription  
Biologie in Unserer Zeit (Biuz)     Hybrid Journal   (Followers: 41)
Biologija     Open Access  
Biology     Open Access   (Followers: 5)
Biology and Philosophy     Hybrid Journal   (Followers: 17)
Biology Bulletin     Hybrid Journal   (Followers: 1)
Biology Bulletin Reviews     Hybrid Journal  

        1 2 3 4 5 6 7 8 | Last

Journal Cover Antonie van Leeuwenhoek
  [SJR: 0.992]   [H-I: 87]   [5 followers]  Follow
    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 1572-9699 - ISSN (Online) 0003-6072
   Published by Springer-Verlag Homepage  [2355 journals]
  • Virulence analysis of Staphylococcus aureus in a rabbit model of infected
           full-thickness wound under negative pressure wound therapy
    • Authors: Daohong Liu; Zhirui Li; Guoqi Wang; Tongtong Li; Lihai Zhang; Peifu Tang
      Pages: 161 - 170
      Abstract: The aim of this study was to evaluate the virulence of Staphylococcus aureus in a controlled animal study using the standard sterile gauze and negative pressure wound therapy (NPWT), including activation of agr, gene expression and production of virulence foctors and depth of bacterial invasion. The tissue specimens were harvested on days 0 (6 h after bacterial inoculation), 2, 4, 6, and 8 at the center of wound beds. Laser scanning confocal microscopy was performed to obtain bioluminescent images which were used to measure the depth of bacterial invasion. The agrA expression of S.aureus and the transcription and production of virulence factors including Eap, Spa and α-toxin were significantly different. The bacterial invasion depth was significantly less with effect of NPWT. The markedly different activation of quorum sensing systems that enable cell-to-cell communication and regulation of numerous colonization and virulence factors result in distinct gene expression and pathogenicity over time in different microenvironment. Thus, the agr system represents a fundamental regulatory paradigm that can encompass different adaptive strategies and accommodate horizontally acquired virulence determinants.
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0938-z
      Issue No: Vol. 111, No. 2 (2018)
       
  • SParticle, an algorithm for the analysis of filamentous microorganisms in
           submerged cultures
    • Authors: Joost Willemse; Ferhat Büke; Dino van Dissel; Sanne Grevink; Dennis Claessen; Gilles P. van Wezel
      Pages: 171 - 182
      Abstract: Streptomycetes are filamentous bacteria that produce a plethora of bioactive natural products and industrial enzymes. Their mycelial lifestyle typically results in high heterogeneity in bioreactors, with morphologies ranging from fragments and open mycelial mats to dense pellets. There is a strong correlation between morphology and production in submerged cultures, with small and open mycelia favouring enzyme production, while most antibiotics are produced mainly in pellets. Here we describe SParticle, a Streptomyces Particle analysis method that combines whole slide imaging with automated image analysis to characterize the morphology of submerged grown Streptomyces cultures. SParticle allows the analysis of over a thousand particles per hour, offering a high throughput method for the imaging and statistical analysis of mycelial morphologies. The software is available as a plugin for the open source software ImageJ and allows users to create custom filters for other microbes. Therefore, SParticle is a widely applicable tool for the analysis of filamentous microorganisms in submerged cultures.
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0939-y
      Issue No: Vol. 111, No. 2 (2018)
       
  • Erratum to: Quantitative physiology and elemental composition of
           Kluyveromyces lactis CBS 2359 during growth on glucose at different
           specific growth rates
    • Authors: Oscar Dias; Thiago O. Basso; Isabel Rocha; Eugénio C. Ferreira; Andreas K. Gombert
      Pages: 197 - 197
      Abstract: In the original publication of the article, the below mentioned errors have appeared. The correct text is provided in this erratum, In the abstract section, the sentence “This dataset serve” should be replaced as “This dataset serves”. Also, the reference “Basso TO, Gomes FS, Lopes ML, et al (2014) Homo- and heterofermentative lactobacilli differently affect sugarcane-based fuel ethanol fermentation. Antonie Van Leeuwenhoek 105:169–177. doi:10.1007/s10482-013-0063-6” should be replaced as “Basso TO, Dario MG, Tonso A, Stambuk BU, Gombert AK (2010) Insufficient uracil supply in fully aerobic chemostat cultures of Saccharomyces cerevisiae leads to respiro-fermentative metabolism and double nutrient-limitation. Biotechnol Lett 32:973–977. doi: 10.1007/s10529-010-0248-2”. Finally, in the Table 2 footnote, “according to (Heijnen 1981)” should be replaced as “according to Heijnen (1981)”.
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0948-x
      Issue No: Vol. 111, No. 2 (2018)
       
  • Influence of aptamer-targeted antibiofilm agents for treatment of
           Pseudomonas aeruginosa biofilms
    • Authors: Sheng Wang; Biyao Mao; Mingxi Wu; Jingjing Liang; Le Deng
      Pages: 199 - 208
      Abstract: Biofilms are bacterial communities consisting of numerous extracellular polymeric substances. Infections caused by biofilm-forming bacteria are considered to be a major threat to health security and so novel approaches to control biofilm are of importance. Aptamers are single-strand nucleic acid molecules that have high selectivity to their targets. Single-walled carbon nanotubes (SWNTs) are common nanomaterials and have been shown to be toxic to bacterial biofilms. The aim of this study was to test whether an aptamer could play a role as targeting agents to enhance the efficiency of anti-biofilm agents. Hence, two complexes (aptamer–SWNTs and aptamer–ciprofloxacin–SWNTs) based on an aptamer which targets Pseudomonas aeruginosa and SWNTs were constructed. Both complexes were assessed against P. aeruginosa biofilms. In vitro tests demonstrated that the aptamer–SWNTs could inhibit ~36% more biofilm formation than SWNTs alone. Similarly, the aptamer–ciprofloxacin–SWNTs had a higher anti-biofilm efficiency than either component or simple mixtures of two components. Our study underscores the potential of aptamers as targeting agents for anti-biofilm compounds, as well as providing a new strategy to control biofilms.
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0941-4
      Issue No: Vol. 111, No. 2 (2018)
       
  • Biodiversity and ecology of flower-associated actinomycetes in different
           flowering stages of Protea repens
    • Authors: Zander R. Human; Casparus J. Crous; Francois Roets; Stephanus N. Venter; Michael J. Wingfield; Z. Wilhelm de Beer
      Pages: 209 - 226
      Abstract: Actinomycete bacteria have previously been reported from reproductive structures (infructescences) of Protea (sugarbush/suikerbos) species, a niche dominated by fungi in the genera Knoxdaviesia and Sporothrix. It is probable that these taxa have symbiotic interactions, but a lack of knowledge regarding their diversity and general ecology precludes their study. We determined the diversity of actinomycetes within Protea repens inflorescence buds, open inflorescences, young and mature infructescences, and leaf litter surrounding these trees. Since the P. repens habitat is fire-prone, we also considered the potential of these bacteria to recolonise infructescences after fire. Actinomycetes were largely absent from flower buds and inflorescences but were consistently present in young and mature infructescences. Two Streptomyces spp. were the most consistent taxa recovered, one of which was also routinely isolated from leaf litter. Lower colonisation rates were evident in samples from a recently burnt site. One of the most consistent taxa isolated from older trees in the unburnt site was absent from this site. Our findings show that P. repens has a distinct community of actinomycetes dominated by a few species. These communities change over time and infructescence developmental stage, season and the age of the host population. Mature infructescences appear to be important sources of inoculum for some of the actinomycetes, seemingly disrupted by fire. Increased fire frequency limiting maturation of P. repens infructescences could thus impact future actinomycete colonisation in the landscape. Streptomyces spp. are likely to share this niche with the ophiostomatoid fungi, which merits further study regarding their interactions and mode of transfer.
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0942-3
      Issue No: Vol. 111, No. 2 (2018)
       
  • Plantactinospora solaniradicis sp. nov., a novel actinomycete isolated
           from the root of a tomato plant ( Solanum lycopersicum L.)
    • Authors: Wenchao Li; Xiaowei Guo; Linlin Shi; Junwei Zhao; Liangliang Yan; Xiaotong Zhong; Chen Zhang; Yufei Chen; Xiangjing Wang; Wensheng Xiang
      Pages: 227 - 235
      Abstract: A Gram-positive, non-motile actinomycete, designated strain NEAU-FJL1T, was isolated from tomato root (Solanum lycopersicum L.) collected from Harbin, Heilongjiang province, north China. The strain formed single spores with smooth surfaces from substrate mycelia. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-FJL1T should be affiliated with the genus Plantactinospora and forms a distinct branch with its close neighbour Plantactinospora soyae NEAU-gxj3T (99.2% sequence similarity). The cell wall was found to contain meso-diaminopimelic acid and the whole cell sugars were identified as xylose, glucose, arabinose and galactose. The predominant menaquinones were identified as MK-10(H6) and MK-10(H4). The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major fatty acids were identified as C15:0, iso-C16:0, anteiso-C17:0, C17:0 and iso-C15:0. With reference to phenotypic characteristics, phylogenetic data and DNA–DNA hybridization results, strain NEAU-FJL1T can be distinguished from its most closely related strain and classified as a new species, for which the name Plantactinospora solaniradicis sp. nov. is proposed. The type strain is NEAU-FJL1T (= DSM 100596T = CGMCC 4.7284T).
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0943-2
      Issue No: Vol. 111, No. 2 (2018)
       
  • Bacterial and archaeal communities inhabiting mussels, sediment and water
           in Indonesian anchialine lakes
    • Authors: D. F. R. Cleary; A. R. M. Polónia
      Pages: 237 - 257
      Abstract: Anchialine lakes are a globally rare and unique ecosystem consisting of saline lakes surrounded by land and isolated from the surrounding marine environment. These lakes host a unique flora and fauna including numerous endemic species. Relatively few studies have, however, studied the prokaryote communities present in these lakes and compared them with the surrounding ‘open water’ marine environment. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach to examine prokaryote (Bacteria and Archaea) composition in three distinct biotopes (sediment, water and the mussel Brachidontes sp.) inhabiting four habitats, namely, three marine lakes and the surrounding marine environment of Berau, Indonesia. Biotope and habitat proved significant predictors of variation in bacterial and archaeal composition and higher taxon abundance. Most bacterial sequences belonged to OTUs assigned to the Proteobacteria. Compared to sediment and water, mussels had relatively high abundances of the classes Mollicutes and Epsilonproteobacteria. Most archaeal sequences, in turn, belonged to OTUs assigned to the Crenarchaeota with the relative abundance of crenarchaeotes highest in mussel samples. For both Bacteria and Archaea, the main variation in composition was between water samples on the one hand and sediment and mussel samples on the other. Sediment and mussels also shared much more OTUs than either shared with water. Abundant bacterial OTUs in mussels were related to organisms previously obtained from corals, oysters and the deepsea mussel Bathymodiolus manusensis. Abundant archaeal OTUs in mussels, in contrast, were closely related to organisms previously obtained from sediment.
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0944-1
      Issue No: Vol. 111, No. 2 (2018)
       
  • Uliginosibacterium sangjuense sp. nov., isolated from sediment of the
           Nakdong River
    • Authors: Ji-Hye Han; Kiwoon Baek; Young-Hee Ahn; Wook Jae Lee; Mi-Hwa Lee
      Pages: 259 - 264
      Abstract: A Gram-negative, aerobic, motile by flagella, and light yellow bacterium, designated SS1-76T, was isolated from sediment of the Nakdong River in Sangju-si, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate SS1-76T belongs to the genus Uliginosibacterium of the family Rhodocyclaceae, exhibiting high sequence similarity with the type strains of Uliginosibacterium gangwonense 5YN10-9T (96.0%) and Uliginosibacterium paludis KBP-13T (94.9%). Strain SS1-76T contains ubiquinone-8 as a respiratory quinone and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0, and C14:0 as major fatty acids. The cellular polar lipids are composed of phosphatidylethanolamine, phosphatidylglycerol, and unidentified aminophospholipids. The DNA G+C content was 65.3 mol%. Phenotypic, chemotaxonomic, and phylogenetic evidence clearly indicated that strain SS1-76T represents a novel species of the genus Uliginosibacterium, for which the name Uliginosibacterium sangjuense sp. nov. is proposed. The type strain is SS1-76T (= KCTC 52159T = JCM 31375T).
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0946-z
      Issue No: Vol. 111, No. 2 (2018)
       
  • Chitinophaga salinisoli sp. nov., isolated from saline soil
    • Authors: Wei-wei Dong; De-long Kong; Qi Zhang; Jie Zhu; Yan-wei Wang; Jin-long Song; Yi-qing Zhou; Xu Jiang; Wei Zhang; Shu-miao Zhao; Zhi-yong Ruan
      Pages: 265 - 273
      Abstract: A novel aerobic bacterium, designated strain LAM9153T, was isolated from a saline soil sample collected from Lingxian County, Shandong Province, China. Cells of strain LAM9153T were observed to be Gram-stain negative, non-motile, non-spore-forming and rod-shaped. The new isolate grew optimally at 30–35 °C, pH 7.0 and 0.5% of NaCl concentration (w/v). According to the phylogenetic analysis based on the 16S rRNA gene sequence, strain LAM9153T shares high similarity with Chitinophaga terrae Gsoil 238T (96.9%) and Chitinophaga niabensis JS 13-10T (95.9%), forming a subcluster with C. terrae Gsoil 238T, Chitinophaga cymbidii R156-2T, C. niabensis JS 13-10T and Chitinophaga soli Gsoil 219T in the phylogenetic tree. The major cellular fatty acids (> 10%) were identified as iso-C15:0, iso-C17:0 3-OH and summed features 3 (C16:1 ω6c and/or C16:1 ω7c). The predominant respiratory quinone was identified as menaquinone MK-7. The polar lipids consisted of phosphatidylethanolamine, aminophospholipid, three unidentified aminolipids and five unidentified lipids. The genomic DNA G+C content was determined to be 53.2 ± 1.6 mol%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain LAM9153T is concluded to represent a novel species of the genus Chitinophaga, for which the name Chitinophaga salinisoli sp. nov. is proposed. The type strain is LAM9153T (= ACCC 19960T = JCM 30847T).
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0947-y
      Issue No: Vol. 111, No. 2 (2018)
       
  • Proteinivorax hydrogeniformans sp. nov., an anaerobic, haloalkaliphilic
           bacterium fermenting proteinaceous compounds with high hydrogen production
           
    • Authors: Yulia Boltyanskaya; Ekaterina Detkova; Nikolay Pimenov; Vadim Kevbrin
      Pages: 275 - 284
      Abstract: A search for the organisms responsible for the degradation of biomass of primary producers in Tanatar lakes resulted in the isolation of a novel anaerobic, haloalkaliphilic microorganism, strain Z-710T. The strain grows on proteinaceous substrates (peptides) but not on proteins. A rather limited range of substances of other classes can be utilised together with tryptone but not individually. An interesting physiological feature of the novel strain is a high capacity for hydrogen production (up to 30% v/v) during proteolytic fermentation. Phylogenetic analysis based on the 16S rRNA gene sequence similarity revealed that the organism can be assigned to the previously described genus Proteinivorax. According to its physiological features and the low DNA–DNA hybridisation level of the strain with the type strain of the only previously described Proteinivorax species—Proteinivorax tanatarense Z-910T—strain Z-710T is described here as representing a novel species with the name Proteinivorax hydrogeniformans sp. nov. The type strain is Z-710T (= DSM 102085T = VKM B-3042T).
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0949-9
      Issue No: Vol. 111, No. 2 (2018)
       
  • Biochemical and genetic analysis of a unique poly(ADP-ribosyl)
           glycohydrolase (PARG) of the pathogenic fungus Fusarium oxysporum f. sp.
           lycopersici
    • Authors: Carlos A. Araiza-Cervantes; Víctor Meza-Carmen; Guadalupe Martínez-Cadena; M. Isabel G. Roncero; Georgina E. Reyna-López; Bernardo Franco
      Pages: 285 - 295
      Abstract: The genome sequence of the plant pathogen Fusarium oxysporum f. sp. lycopersici contains a single gene encoding a predicted poly(ADP-ribose) glycohydrolase (FOXG_05947.2, PARG). Here, we assessed whether this gene has a role as a global regulator of DNA repair or in virulence as an ADP ribosylating toxin homologue of bacteria. The PARG protein was purified after expressing its encoding gene in Escherichia coli. Its inhibition by 6,9-diamino-2-ethoxyacridine lactate monohydrate and tannins was similar to its human orthologue that is involved in DNA repair. A deletion strain of F. oxysporum f. sp. lycopersici showed no growth defects and was not affected in pathogenicity. Together, our results indicate that the PARG protein of F. oxysporum f. sp. lycopersici is involved in DNA repair and does not act in pathogenicity as an effector.
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0951-2
      Issue No: Vol. 111, No. 2 (2018)
       
  • A protein complex bearing an oxidase with napthalene dihydrodiol
           dehydrogenase activity is induced in Mucor circinelloides strain YR-1
           during growth on polycyclic aromatic compounds
    • Authors: Jazmín Areli Álvarez Copado; Roberto Zazueta Sandoval; Areli Durón Castellanos; Felipe Padilla-Vaca; Bernardo Franco
      Pages: 297 - 309
      Abstract: Fungi are organisms capable of growing in a myriad of conditions and respond to counteract environmental cues. Several locations in the world are polluted with oil and its derivatives, and some microorganisms tolerant to these compounds have been isolated. Some fungi can grow in the presence of molecules such as polycyclic aromatic hydrocarbons as sole carbon sources. In this report, we further characterized the induced enzymes with phenanthrene from Mucor circinelloides YR-1 strain, isolated from a polluted field near a petrochemical facility in México. We identified a putative oxidase that is induced when growth with phenanthrene as sole carbon source at a pH of 8.5 and is NADP+ dependent. We show that this enzyme bears naphthalene dihydrodiol dehydrogenase activity with substrate preference for the cis-naphthalene over the trans-naphthalene, with an optimal pH in the range of 8–10. Mass spectrometry analysis revealed that the induced enzyme belongs to the NADP+ oxidase family enzymes with the typical Rossmann-fold for NADP+ binding. This enzyme seems to form a high molecular weight structure (~ 541 kDa) and with a monomer of 57 kDa, suggesting that the multimer is constituted of 10 subunits. Our findings contribute to understanding of the roles that dihydrodiol dehydrogenases have in organisms exposed to toxic compounds in the environment and can regulate their expression.
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-017-0950-3
      Issue No: Vol. 111, No. 2 (2018)
       
  • Sediminibacillus massiliensis sp. nov., a moderately halophilic,
           Gram-positive bacterium isolated from a stool sample of a young Senegalese
           man
    • Authors: Bruno Senghor; Hubert Bassène; Saber Khelaifia; Catherine Robert; Pierre-Edouard Fournier; Raymond Ruimy; Cheikh Sokhna; Didier Raoult; Jean-Christophe Lagier
      Abstract: A Gram-positive, moderately halophilic bacterium, referred to as strain Marseille-P3518T, was isolated from a stool sample with 2% NaCl concentration from a healthy 15-year-old male living in Dielmo, a village in Senegal. Cells are aerobic, rod-shaped and motile and display endospore formation. Strain Marseille-P3518T can grow in a medium with 0–20% (w/v) sodium chloride (optimally at 5–7.5% w/v). The major fatty acids were 12-methyl-tetradecanoic acid (45.8%), 13-methyl-tetradecanoic acid (26.9%) and 12-methyl-tridecanoic acid (12.8%). The genome is 4,347,479 bp long with 42.1% G+C content. It contains 4282 protein-coding and 107 RNA genes. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain Marseille-P3518T is a member of the Bacillaceae family and is closely related to Sediminibacillus albus (97.4% gene sequence similarity). Strain Marseille-P3518T was clearly differentiated from its phylogenetic neighbors on the basis of phenotypic and genotypic features. Strain Marseille-P3518T is, therefore, considered to be a novel representative of the genus Sediminibacillus, for which the name Sediminibacillus massiliensis sp. nov. is proposed, and the type strain is Marseille-P3518T (CSUR P3518T, DSM69894).
      PubDate: 2018-02-07
      DOI: 10.1007/s10482-018-1032-x
       
  • Formal description of Mycobacterium neglectum sp. nov. and Mycobacterium
           palauense sp. nov., rapidly growing actinobacteria
    • Authors: Imen Nouioui; Lorena Carro; Vartul Sangal; Marlen Jando; José Mariano Igual; Michael Goodfellow; Hans-Peter Klenk
      Abstract: The taxonomic positions of two fast growing mycobacteria (CECT 8778T and CECT 8779T) were established using a polyphasic approach. The strains were shown to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Mycobacterium. Multi-locus sequence analyses (MLSA) show that strain CECT 8778T forms a well-supported clade together with the type strains of Mycobacterium aurum, Mycobacterium austroafricanum and Mycobacterium vanbaalenii while strain CECT 8779T presents as a distinct branch that is well separated from its near phylogenetic neighbours; it is also apparent from the MLSA genetic distances that these strains are most closely related to the type strains of Mycobacterium mageritense and M. vanbaalenii, respectively. Digital DNA:DNA hybridization and average nucleotide identity values between each of the strains and its close phylogenetic neighbour are below the 70 and 96% threshold values for definition of prokaryotic species; these results are underpinned by corresponding phenotypic data. Based upon the consensus of the phenotypic and phylogenetic analyses, it can be concluded that the two strains represent novel species within the genus Mycobacterium for which the following names are proposed: Mycobacterium neglectum sp. nov., with the type strain CECT 8778T (BN 3150T = DSM 44756T) and Mycobacterium palauense sp. nov., with the type strain CECT 8779T (= DSM 44914T).
      PubDate: 2018-02-05
      DOI: 10.1007/s10482-018-1029-5
       
  • Lentibacillus alimentarius sp. nov., isolated from Myeolchi-jeotgal, a
           traditional Korean high-salt fermented anchovy
    • Authors: Aravind Sundararaman; Sathiyaraj Srinivasan; Jong-Hoon Lee; Sang-Seob Lee
      Abstract: A Gram-positive, motile, endospore-forming, rod-shaped bacterium, designated strain M2024T, was isolated from Myeolchi-jeotgal, a traditional Korean high-salt fermented anchovy and was characterised using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain M2024T belongs to the genus Lentibacillus in the family Bacillaceae of the Firmicutes. The 16S rRNA gene sequence analysis showed that strain M2024T is closely related to Lentibacillus populi WD4L-1T (95.5%), Lentibacillus garicola SL-MJ1T (95.2%) and Virgibacillus siamensis MS3-4T (95.1%). The chemotaxonomic properties of strain M2024T are consistent with those of members of the genus Lentibacillus: the quinone system has MK-7 as the predominant menaquinone and anteiso-C15:0 and anteiso-C17:0 are the predominant cellular fatty acids. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was determined to be 36.2 mol%. Differential phenotypic properties compared with closely related type strains support the conclusion that strain M2024T can be separated from previously described members of the genus Lentibacillus. The strain thus represents a novel species in this genus, for which the name Lentibacillus alimentarius sp. nov. is proposed. The type strain is M2024T (= KEMB 9001-124T = JCM 16521T).
      PubDate: 2018-02-03
      DOI: 10.1007/s10482-017-1006-4
       
  • Effect of nicotine from tobacco root exudates on chemotaxis, growth,
           biocontrol efficiency, and colonization by Pseudomonas   aeruginosa
           NXHG29
    • Authors: Li Ma; Shuai Chao Zheng; Ti Kun Zhang; Zi Yi Liu; Xue Jian Wang; Xing Kui Zhou; Cheng Gang Yang; Jin Ling Duo; Ming He Mo
      Abstract: Accumulated evidence suggests that root exudates have a major role in mediating plant–microbe interactions in the rhizosphere. Here, we characterized tobacco root exudates (TREs) by GC–MS and nicotine, scopoletin, and octadecane were identified as three main components of TREs. Qualitative and quantitative chemotaxis assays revealed that Pseudomonas aeruginosa NXHG29 with antagonistic activity displayed positive chemotactic responses towards TREs and their three main components (nicotine, scopoletin, octadecane) and its enhanced chemotaxis were induced by these substances in a concentration-dependent manner. Furthermore, following GC–MS and chemotaxis analysis, nicotine was selected as the target for evaluation of the effect on NXHG29 regarding antagonism, growth, root colonization and biocontrol efficiency. Results of in vitro studies showed that nicotine as a sole carbon source could enhance growth of NXHG29 and significantly increased the antagonism of NXHG29. We also demonstrated that nicotine exerted enhancing effects on the colonization ability of NXHG29 on tobacco roots by combining CLSM observations with investigation of population level dynamics by selective dilution plating method. Results from greenhouse experiments suggested nicotine exhibited stimulatory effects on the biocontrol efficiency of NXHG29 against bacterial wilt and black shank on tobacco. The stimulatory effect of nicotine was affected by the concentration and timing of nicotine application and further supported by the results of population level of NXHG29 on tobacco roots. This is the first report on the enhancement effect of nicotine from TREs on an antagonistic bacterium for its root colonization, control of soil-borne pathogens, regarding the chemotaxis and in vitro antagonism and growth.
      PubDate: 2018-02-03
      DOI: 10.1007/s10482-018-1035-7
       
  • The ‘gifted’ actinomycete Streptomyces leeuwenhoekii
    • Authors: Jean Franco Castro; Valeria Razmilic; Juan Pablo Gomez-Escribano; Barbara Andrews; Juan Asenjo; Mervyn Bibb
      Abstract: Streptomyces leeuwenhoekii strains C34T, C38, C58 and C79 were isolated from a soil sample collected from the Chaxa Lagoon, located in the Salar de Atacama in northern Chile. These streptomycetes produce a variety of new specialised metabolites with antibiotic, anti-cancer and anti-inflammatory activities. Moreover, genome mining performed on two of these strains has revealed the presence of biosynthetic gene clusters with the potential to produce new specialised metabolites. This review focusses on this new clade of Streptomyces strains, summarises the literature and presents new information on strain C34T.
      PubDate: 2018-02-03
      DOI: 10.1007/s10482-018-1034-8
       
  • Metabolic modelling and flux analysis of microorganisms from the Atacama
           Desert used in biotechnological processes
    • Authors: Valeria Razmilic; Jean Franco Castro; Francisca Marchant; Juan A. Asenjo; Barbara Andrews
      Abstract: Metabolic modelling is a useful tool that enables the rational design of metabolic engineering experiments and the study of the unique capabilities of biotechnologically important microorganisms. The extreme abiotic conditions of the Atacama Desert have selected microbial diversity with exceptional characteristics that can be applied in the mining industry for bioleaching processes and for production of specialised metabolites with antimicrobial, antifungal, antiviral, antitumoral, among other activities. In this review we summarise the scientific data available of the use of metabolic modelling and flux analysis to improve the performance of Atacama Desert microorganisms in biotechnological applications.
      PubDate: 2018-02-02
      DOI: 10.1007/s10482-018-1031-y
       
  • Ponticaulis profundi sp. nov. isolated from a deep-sea seamount
    • Authors: Ya-Wen Sun; Jie Liu; De-Chao Zhang
      Abstract: A Gram-stain negative, rod-shaped, strictly aerobic, motile bacterial strain, designated YC239T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YC239T is related to the genus Ponticaulis and has high 16S rRNA gene sequence similarity with the type strain of Ponticaulis koreensis GSW-23T (97.9%). The predominant cellular fatty acids were C18:1ω7c, C16:0, C17:0 and C17:1ω6c. Strain YC239T had Q-10 as the predominant ubiquinone. The polar lipid profile contained phosphatidylglycerol, two unidentified aminolipids and six unidentified polar lipids. The genomic DNA G+C content of strain YC239T was 52.8 mol%. Strain YC239T shared DNA relatedness of 38% with Ponticaulis koreensis KCTC 22146T. On the basis of the evidence presented in this study, strain YC239T represents a novel species of the genus Ponticaulis, for which we propose the name Ponticaulis profundi sp. nov. (type strain YC239T = KACC 19027T = CGMCC 1.15741T).
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-018-1027-7
       
  • Lithobiontic life: “Atacama rocks are well and alive”
    • Authors: Benito Gómez-Silva
      Abstract: Our knowledge on the Microbiology of the Atacama Desert has increased steadily and substantially during the last two decades. This information now supports a paradigmatic change on the Atacama Desert from a sterile, uninhabitable territory to a hyperarid region colonized by a rich microbiota that includes extremophiles and extreme-tolerant microorganisms. Also, extensive reports are available on the prevalent physical and chemical environmental conditions, ecological niches and, the abundance, diversity and organization of the microbial life in the Atacama Desert. This territory is a highly desiccated environment due to the absence of regular rain events. Liquid water scarcity is the most serious environmental factor affecting the Atacama Desert microorganisms. The intense solar irradiation in this region contributes, in a synergistic fashion with desiccation, to limit the survival and growth of the microbial life. In order to overcome these two extreme conditions, successful microorganisms, organized as microbial consortia, take advantage of (a) the physical characteristics of lithic habitats, which provide sites for colonization on, within or below the rock substrate, the attenuation and filtration of the intense solar irradiation and, the collection of liquid water from incoming fog formations and by water vapour condensation and deliquescence on or within their surfaces, and (b) the biological adaptations of members of the microbial communities that allow them to synthesize hydrophilic macromolecules, antioxidants and UV-light absorbents. Lithic habitats have been considered specialized shelters where life forms can reach protection at environments subjected to extremes of desiccation and solar irradiation, here on Earth or elsewhere. This review is an overview of part of the scientific information collected on lithobionts from the Atacama Desert, their rock substrates and their strategies to cope with extremes of desiccation and intense photosynthetic active radiation and UV irradiations.
      PubDate: 2018-02-01
      DOI: 10.1007/s10482-018-1033-9
       
 
 
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