819 research outputs found

    Caldolysin, a highly active protease from an extremely Thermophilic Bacterium

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    Proteases comprise a significant proportion of those proteins which have been subject to detailed characterisation (amino acid sequence and high resolution crystallographic analysis). The extent of research interest in proteolytic enzymes reflects both their historical status, and the practical advantages of proteases as research subjects (available in quantity, extracellular etc.) widely occurring

    The industrial potential of enzymes from extremely thermophilic bacteria

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    The thermal regions of the central North Island of New Zealand are some of the most extensive in the world. In addition, they are readily accessible and contain a diversity of ecological habitats, including a large number at 100°C. These areas are regarded as an important tourist attraction, and as a source of geothermal power, It is now clear that they also contain an important and unique genetic resource

    Diverse hypolithic refuge communities in the McMurdo Dry Valleys

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    Hyper-arid deserts present extreme challenges to life. The environmental buffering provided by quartz and other translucent rocks allows hypolithic microbial communities to develop on sub-soil surfaces of such rocks. These refuge communities have been reported, for many locations worldwide, to be predominantly cyanobacterial in nature. Here we report the discovery in Antarctica’s hyper-arid McMurdo Dry Valleys of three clearly distinguishable types of hypolithic community. Based on gross colonization morphology and identification of dominant taxa, we have classified hypolithic communities as Type I (cyanobacterial dominated), Type II (fungal dominated) and Type III (moss dominated). This discovery supports a growing awareness of the high biocomplexity in Antarctic deserts, emphasizes the possible importance of cryptic microbial communities in nutrient cycling and provides evidence for possible successional community processes within a cold arid landscape

    Flashy flagella: flagellin modification is relatively common and highly versatile among the Enterobacteriaceae

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    Schematic diagrams of inserts within the fliDCAZ loci of FGI−/FMI− Enterobacteriaceae. Flanking genes are indicated by yellow arrows, predicted phage genes by blue arrows, fimbrial biogenesis genes by grey arrows and sugar/amino acid transporter genes by orange arrows. Black arrows indicate predicted transposase or endonuclease genes, while the red arrows indicate genes with disrupted reading frames. The flagellin glycan biosynthetic genes in the FGI+ strains E. tracheiphila Buff/PSU-1 are indicated by green arrows, upstream of the predicted phage integration site. (TIF 471 kb

    Protection of Antarctic microbial communities - 'out of sight, out of mind'

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    Recent advances in molecular biology techniques have shown the presence of diverse microbial communities and endemic species in Antarctica. Endemic microbes may be a potential source of novel biotechnologically important compounds, including, for example, new antibiotics. Thus, the scientific and biotechnological value of Antarctic terrestrial microbial habitats can be compromised by human visitation to a greater extent than previously realized. The ever-increasing human footprint in Antarctica makes consideration of this topic more pressing, as the number of locations known to be pristine habitats, where increasingly sophisticated cutting-edge research techniques may be used to their full potential, declines. Examination of the Protected Areas system of the Antarctic Treaty shows that microbial habitats are generally poorly protected. No other continent on Earth is dominated to the same degree by microbial species, and real opportunities exist to develop new ways of conceptualising and implementing conservation of microbial biogeography on a continental scale. Here we highlight potential threats both to the conservation of terrestrial microbial ecosystems, and to future scientific research requiring their study

    Micro-eukaryotic diversity in hypolithons from Miers Valley, Antarctica

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    The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This study represents the first investigation of micro-eukaryotic communities in all three hypolith types. Here we show that Antarctic hypoliths support extensive populations of novel uncharacterized bryophyta, fungi and protists and suggest that well known producer-decomposer-predator interactions may create the necessary conditions for hypolithic productivity in Antarctic deserts

    Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts

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    Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the twometagenomeswere identified. The Antarctic hypolithicmetagenome displayed a high number of sequences assigned to sigma factors, replication,recombination andrepair, translation, ribosomal structure,andbiogenesis. In contrast, theNamibDesert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significantdivergence inthe geneticdeterminantsof aminoacidandnucleotidemetabolismbetween these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes.Fil: Le, Phuong Thi. University of Pretoria; Sudáfrica. Vlaams Instituut voor Biotechnologie; Bélgica. University of Ghent; BélgicaFil: Makhalanyane, Thulani P.. University of Pretoria; SudáfricaFil: Guerrero, Leandro Demián. University of Pretoria; Sudáfrica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Vikram, Surendra. University of Pretoria; SudáfricaFil: Van De Peer, Yves. University of Pretoria; Sudáfrica. Vlaams Instituut voor Biotechnologie; Bélgica. University of Ghent; BélgicaFil: Cowan, Don A.. University of Pretoria; Sudáfric

    A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils

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    Background: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity. Methods: We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs. Results: In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and beta-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r=-0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events. Conclusions: ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments

    Foliar fungi of the enigmatic desert plant Welwitschia mirabilis show little adaptation to their unique host plant

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    Foliar fungi, especially endophytic fungi, constitute an important part of the microbiome of plants. Yet little is known about the composition of these communities. In this study, we isolated fungi from leaf tissues of the desert plant&nbsp;Welwitschia mirabilis&nbsp;to determine the culturable diversity of the foliar fungal community. The isolated fungal taxa, which grouped into 17 distinct lineages, were identified by sequencing elongation factor 1 alpha, beta-tubulin 1, beta-tubulin 2 and the internal transcribed spacer region. The culturable community was mainly composed of cosmopolitan fungal genera despite the unique taxonomic position of the plant and its geographic isolation. To test for endemism in two of the common fungal genera,&nbsp;Alternaria&nbsp;and&nbsp;Aureobasidium, we built haplotype networks using a global data set. Even this broad data set showed little evidence for specialisation within this unique host or its geographical location. The data suggest that the culturable members of communities of leaf-associated fungi in habitats with little plant coverage, such as the Namib Desert, are mainly established by long-distance aerially distributed fungal inocula and few of these taxa co-evolve with the host within the habitat.Significance: The culturable members of fungal communities associated with an ecological and evolutionary isolated plant have not co-speciated with their hosts, but to a large extent are composed of globally distributed fungal species. Harsh environmental conditions and the geographic isolation of host plants seem to favour ubiquitous fungal species over more specialist fungal species

    Diversity of Frankia in root nodules of six Morella sp. from the Cape flora of South Africa

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    Africa hosts numerous endemic actinorhizal plants from the genus Morella, but the diversity of their Frankia endosymbionts has never been explored. The diversity of Frankia in root nodules collected from natural stands of six Morella species within the Cape flora of South Africa was investigated. The diversity of Frankia in root nodules collected from natural stands of six Morella species within the Cape flora of South Africa was investigated by comparative nitrogenase (nifH) gene sequence analysis. Gene sequences assigned nodular strains to both cluster I (Alnus hostinfection group) and cluster III (Elaeagnus host-infection group), with sequences from both groups recovered from three hosts: M. intergra, M. diversifolia and M. quercifolia. Cluster I sequences were found in nodules from acidic soils exclusively. Frankia strains representing both groups were isolated and characterized by 16S rRNA and nifH analysis. This study is the first to investigate the diversity of Frankia associated with endemic African actinorhizal species in their natural habitats, and to report isolation of Frankia strains from African Morella.The South African National Research Foundation and University of Pretoria Genomics Research Institute.http://link.springer.com/journal/111042017-04-30hb2016Genetic
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