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Sample records for bacterial species diversity

  1. Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems.

    Science.gov (United States)

    Reverter, Miriam; Sasal, Pierre; Tapissier-Bontemps, N; Lecchini, D; Suzuki, M

    2017-06-01

    While recent studies have suggested that fish mucus microbiota play an important role in homeostasis and prevention of infections, very few studies have investigated the bacterial communities of gill mucus. We characterised the gill mucus bacterial communities of four butterflyfish species and although the bacterial diversity of gill mucus varied significantly between species, Shannon diversities were high (H = 3.7-5.7) in all species. Microbiota composition differed between butterflyfishes, with Chaetodon lunulatus and C. ornatissimus having the most similar bacterial communities, which differed significantly from C. vagabundus and C. reticulatus. The core bacterial community of all species consisted of mainly Proteobacteria followed by Actinobacteria and Firmicutes. Chaetodonlunulatus and C. ornatissimus bacterial communities were mostly dominated by Gammaproteobacteria with Vibrio as the most abundant genus. Chaetodonvagabundus and C. reticulatus presented similar abundances of Gammaproteobacteria and Alphaproteobacteria, which were well represented by Acinetobacter and Paracoccus, respectively. In conclusion, our results indicate that different fish species present specific bacterial assemblages. Finally, as mucus layers are nutrient hotspots for heterotrophic bacteria living in oligotrophic environments, such as coral reef waters, the high bacterial diversity found in butterflyfish gill mucus might indicate external fish mucus surfaces act as a reservoir of coral reef bacterial diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

    Science.gov (United States)

    Bhatnagar, Srijak; Eisen, Jonathan A.; Kopp, Artyom

    2011-01-01

    Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in

  3. Coral-Associated Bacterial Diversity is Conserved Across Two Deep-Sea Anthothela Species

    Directory of Open Access Journals (Sweden)

    Stephanie Nichole Lawler

    2016-04-01

    Full Text Available Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12 and Baltimore Canyons (n = 11 from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp. and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp. had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

  4. Diversity and Phylogenetic Analyses of Bacterial Symbionts in Three Whitefly Species from Southeast Europe

    Science.gov (United States)

    Skaljac, Marisa; Zanic, Katja; Puizina, Jasna; Lepen Pleic, Ivana; Ghanim, Murad

    2017-01-01

    Bemisia tabaci (Gennadius), Trialeurodes vaporariorum (Westwood), and Siphoninus phillyreae (Haliday) are whitefly species that harm agricultural crops in many regions of the world. These insects live in close association with bacterial symbionts that affect host fitness and adaptation to the environment. In the current study, we surveyed the infection of whitefly populations in Southeast Europe by various bacterial symbionts and performed phylogenetic analyses on the different symbionts detected. Arsenophonus and Hamiltonella were the most prevalent symbionts in all three whitefly species. Rickettsia was found to infect mainly B. tabaci, while Wolbachia mainly infected both B. tabaci and S. phillyreae. Furthermore, Cardinium was rarely found in the investigated whitefly populations, while Fritschea was never found in any of the whitefly species tested. Phylogenetic analyses revealed a diversity of several symbionts (e.g., Hamiltonella, Arsenophonus, Rickettsia), which appeared in several clades. Reproductively isolated B. tabaci and T. vaporariorum shared the same (or highly similar) Hamiltonella and Arsenophonus, while these symbionts were distinctive in S. phillyreae. Interestingly, Arsenophonus from S. phillyreae did not cluster with any of the reported sequences, which could indicate the presence of Arsenophonus, not previously associated with whiteflies. In this study, symbionts (Wolbachia, Rickettsia, and Cardinium) known to infect a wide range of insects each clustered in the same clades independently of the whitefly species. These results indicate horizontal transmission of bacterial symbionts between reproductively isolated whitefly species, a mechanism that can establish new infections that did not previously exist in whiteflies. PMID:29053633

  5. Diversity and Phylogenetic Analyses of Bacterial Symbionts in Three Whitefly Species from Southeast Europe

    Directory of Open Access Journals (Sweden)

    Marisa Skaljac

    2017-10-01

    Full Text Available Bemisia tabaci (Gennadius, Trialeurodes vaporariorum (Westwood, and Siphoninus phillyreae (Haliday are whitefly species that harm agricultural crops in many regions of the world. These insects live in close association with bacterial symbionts that affect host fitness and adaptation to the environment. In the current study, we surveyed the infection of whitefly populations in Southeast Europe by various bacterial symbionts and performed phylogenetic analyses on the different symbionts detected. Arsenophonus and Hamiltonella were the most prevalent symbionts in all three whitefly species. Rickettsia was found to infect mainly B. tabaci, while Wolbachia mainly infected both B. tabaci and S. phillyreae. Furthermore, Cardinium was rarely found in the investigated whitefly populations, while Fritschea was never found in any of the whitefly species tested. Phylogenetic analyses revealed a diversity of several symbionts (e.g., Hamiltonella, Arsenophonus, Rickettsia, which appeared in several clades. Reproductively isolated B. tabaci and T. vaporariorum shared the same (or highly similar Hamiltonella and Arsenophonus, while these symbionts were distinctive in S. phillyreae. Interestingly, Arsenophonus from S. phillyreae did not cluster with any of the reported sequences, which could indicate the presence of Arsenophonus, not previously associated with whiteflies. In this study, symbionts (Wolbachia, Rickettsia, and Cardinium known to infect a wide range of insects each clustered in the same clades independently of the whitefly species. These results indicate horizontal transmission of bacterial symbionts between reproductively isolated whitefly species, a mechanism that can establish new infections that did not previously exist in whiteflies.

  6. Cuticles of European and American lobsters harbor diverse bacterial species and differ in disease susceptibility.

    Science.gov (United States)

    Whitten, Miranda M A; Davies, Charlotte E; Kim, Anita; Tlusty, Michael; Wootton, Emma C; Chistoserdov, Andrei; Rowley, Andrew F

    2014-06-01

    Diseases of lobster shells have a significant impact on fishing industries but the risk of disease transmission between different lobster species has yet to be properly investigated. This study compared bacterial biofilm communities from American (Homarus americanus) and European lobsters (H. gammarus), to assess both healthy cuticle and diseased cuticle during lesion formation. Culture-independent molecular techniques revealed diversity in the bacterial communities of cuticle biofilms both within and between the two lobster species, and identified three bacterial genera associated with shell lesions plus two putative beneficial bacterial species (detected exclusively in healthy cuticle or healing damaged cuticle). In an experimental aquarium shared between American and European lobsters, heterospecific transmission of potentially pathogenic bacteria appeared to be very limited; however, the claws of European lobsters were more likely to develop lesions when reared in the presence of American lobsters. Aquarium biofilms were also examined but revealed no candidate pathogens for environmental transmission. Aquimarina sp. 'homaria' (a potential pathogen associated with a severe epizootic form of shell disease) was detected at a much higher prevalence among American than European lobsters, but its presence correlated more with exacerbation of existing lesions rather than with lesion initiation. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  7. Species Diversity and Functional Prediction of Surface Bacterial Communities on Aging Flue-Cured Tobaccos.

    Science.gov (United States)

    Wang, Fan; Zhao, Hongwei; Xiang, Haiying; Wu, Lijun; Men, Xiao; Qi, Chang; Chen, Guoqiang; Zhang, Haibo; Wang, Yi; Xian, Mo

    2018-06-05

    Microbes on aging flue-cured tobaccos (ATFs) improve the aroma and other qualities desirable in products. Understanding the relevant organisms would picture microbial community diversity, metabolic potential, and their applications. However, limited efforts have been made on characterizing the microbial quality and functional profiling. Herein, we present our investigation of the bacterial diversity and predicted potential genetic capability of the bacteria from two AFTs using 16S rRNA gene sequences and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) software. The results show that dominant bacteria from AFT surfaces were classified into 48 genera, 36 families, and 7 phyla. In addition, Bacillus spp. was found prevalent on both ATFs. Furthermore, PICRUSt predictions of bacterial community functions revealed many attractive metabolic capacities in the AFT microbiota, including several involved in the biosynthesis of flavors and fragrances and the degradation of harmful compounds, such as nicotine and nitrite. These results provide insights into the importance of AFT bacteria in determining product qualities and indicate specific microbial species with predicted enzymatic capabilities for the production of high-efficiency flavors, the degradation of undesirable compounds, and the provision of nicotine and nitrite tolerance which suggest fruitful areas of investigation into the manipulation of AFT microbiota for AFT and other product improvements.

  8. Diversity and Phylogenetic Analyses of Bacterial Symbionts in Three Whitefly Species from Southeast Europe

    OpenAIRE

    Skaljac, Marisa; Kanakala, Surapathrudu; Zanic, Katja; Puizina, Jasna; Lepen Pleic, Ivana; Ghanim, Murad

    2017-01-01

    Bemisia tabaci (Gennadius), Trialeurodes vaporariorum (Westwood), and Siphoninus phillyreae (Haliday) are whitefly species that harm agricultural crops in many regions of the world. These insects live in close association with bacterial symbionts that affect host fitness and adaptation to the environment. In the current study, we surveyed the infection of whitefly populations in Southeast Europe by various bacterial symbionts and performed phylogenetic analyses on the different symbionts dete...

  9. Bacterial diversity of bacteriomes and organs of reproductive, digestive and excretory systems in two cicada species (Hemiptera: Cicadidae).

    Science.gov (United States)

    Zheng, Zhou; Wang, Dandan; He, Hong; Wei, Cong

    2017-01-01

    Cicadas form intimate symbioses with bacteria to obtain nutrients that are scarce in the xylem fluid they feed on. The obligate symbionts in cicadas are purportedly confined to specialized bacteriomes, but knowledge of bacterial communities associated with cicadas is limited. Bacterial communities in the bacteriomes and organs of reproductive, digestive and excretory systems of two cicada species (Platypleura kaempferi and Meimuna mongolica) were investigated using different methods, and the bacterial diversity and distribution patterns of dominant bacteria in different tissues were compared. Within each species, the bacterial communities of testes are significantly different from those of bacteriomes and ovaries. The dominant endosymbiont Candidatus Sulcia muelleri is found not only in the bacteriomes and reproductive organs, but also in the "filter chamber + conical segment" of both species. The transmission mode of this endosymbiont in the alimentary canal and its effect on physiological processes merits further study. A novel bacterium of Rhizobiales, showing ~80% similarity to Candidatus Hodgkinia cicadicola, is dominant in the bacteriomes and ovaries of P. kaempferi. Given that the genome of H. cicadicola exhibits rapid sequence evolution, it is possible that this novel bacterium is a related endosymbiont with beneficial trophic functions similar to that of H. cicadicola in some other cicadas. Failure to detect H. cicadicola in M. mongolica suggests that it has been subsequently replaced by another bacterium, a yeast or gut microbiota which compensates for the loss of H. cicadicola. The distribution of this novel Rhizobiales species in other cicadas and its identification require further investigation to help establish the definition of the bacterial genus Candidatus Hodgkinia and to provide more information on sequence divergence of related endosymbionts of cicadas. Our results highlight the complex bacterial communities of cicadas, and are informative for

  10. Bacterial diversity of bacteriomes and organs of reproductive, digestive and excretory systems in two cicada species (Hemiptera: Cicadidae.

    Directory of Open Access Journals (Sweden)

    Zhou Zheng

    Full Text Available Cicadas form intimate symbioses with bacteria to obtain nutrients that are scarce in the xylem fluid they feed on. The obligate symbionts in cicadas are purportedly confined to specialized bacteriomes, but knowledge of bacterial communities associated with cicadas is limited. Bacterial communities in the bacteriomes and organs of reproductive, digestive and excretory systems of two cicada species (Platypleura kaempferi and Meimuna mongolica were investigated using different methods, and the bacterial diversity and distribution patterns of dominant bacteria in different tissues were compared. Within each species, the bacterial communities of testes are significantly different from those of bacteriomes and ovaries. The dominant endosymbiont Candidatus Sulcia muelleri is found not only in the bacteriomes and reproductive organs, but also in the "filter chamber + conical segment" of both species. The transmission mode of this endosymbiont in the alimentary canal and its effect on physiological processes merits further study. A novel bacterium of Rhizobiales, showing ~80% similarity to Candidatus Hodgkinia cicadicola, is dominant in the bacteriomes and ovaries of P. kaempferi. Given that the genome of H. cicadicola exhibits rapid sequence evolution, it is possible that this novel bacterium is a related endosymbiont with beneficial trophic functions similar to that of H. cicadicola in some other cicadas. Failure to detect H. cicadicola in M. mongolica suggests that it has been subsequently replaced by another bacterium, a yeast or gut microbiota which compensates for the loss of H. cicadicola. The distribution of this novel Rhizobiales species in other cicadas and its identification require further investigation to help establish the definition of the bacterial genus Candidatus Hodgkinia and to provide more information on sequence divergence of related endosymbionts of cicadas. Our results highlight the complex bacterial communities of cicadas, and

  11. Diversity and distribution of culturable lactic acid bacterial species in Indonesian Sayur Asin.

    Science.gov (United States)

    Mangunwardoyo, Wibowo; Abinawanto; Salamah, Andi; Sukara, Endang; Sulistiani; Dinoto, Achmad

    2016-08-01

    Lactic acid bacteria (LAB) play important roles in processing of Sayur Asin (spontaneously fermented mustard). Unfortunately, information about LAB in Indonesian Sayur Asin, prepared by traditional manufactures which is important as baseline data for maintenance of food quality and safety, is unclear. The aim of this study was to describe the diversity and distribution of culturable lactic acid bacteria in Sayur Asin of Indonesia. Four Sayur Asin samples (fermentation liquor and fermented mustard) were collected at harvesting times (3-7 days after fermentation) from two traditional manufactures in Tulung Agung (TA) and Kediri (KDR), East Java provinces, Indonesia. LAB strains were isolated by using MRS agar method supplemented with 1% CaCO 3 and characterized morphologically. Identification of the strains was performed basedon 16S rDNA analysis and the phylogenetic tree was drawn to understand the phylogenetic relationship of the collected strains. Different profiles were detected in total count of the plates, salinity and pH of fermenting liquor of Sayur Asin in TA and KDR provinces. A total of 172 LAB isolates were successfully isolated and identified based on their 16S rDNA sequences. Phylogenetic analysis of 27 representative LAB strains from Sayur Asin showed that these strains belonged to 5 distinct species namely Lactobacilus farciminis (N=32), L. fermentum (N=4), L. namurensis (N=15), L. plantarum (N=118) and L. parafarraginis (N=1). Strains D5-S-2013 and B4-S-2013 showed a close phylogenetic relationship with L. composti and L. paralimentarius, respectively where as the sequence had slightly lower similarity of lower than 99%, suggesting that they may be classified into novel species and need further investigation due to exhibition of significant differences in their nucleotide sequences. Lactobacillus plantarum was found being dominant in all sayur asin samples. Lactobacilli were recognized as the major group of lactic acid bacteria in Sayur Asin

  12. Growth promotion of Lactuca sativa in response to volatile organic compounds emitted from diverse bacterial species.

    Science.gov (United States)

    Fincheira, Paola; Venthur, Herbert; Mutis, Ana; Parada, Maribel; Quiroz, Andrés

    2016-12-01

    Agrochemicals are currently used in horticulture to increase crop production. Nevertheless, their indiscriminate use is a relevant issue for environmental and legal aspects. Alternative tools for reducing fertilizers and synthetic phytohormones are being investigated, such as the use of volatile organic compounds (VOCs) as growth inducers. Some soil bacteria, such as Pseudomonas and Bacillus, stimulate Arabidopsis and tobacco growth by releasing VOCs, but their effects on vegetables have not been investigated. Lactuca sativa was used as model vegetable to investigate bacterial VOCs as growth inducers. We selected 10 bacteria strains, belonging to Bacillus, Staphylococcus and Serratia genera that are able to produce 3-hydroxy-2-butanone (acetoin), a compound with proven growth promoting activity. Two-day old-seedlings of L. sativa were exposed to VOCs emitted by the selected bacteria grown in different media cultures for 7 days. The results showed that the VOCs released from the bacteria elicited an increase in the number of lateral roots, dry weight, root growth and shoot length, depending on the media used. Three Bacillus strains, BCT53, BCT9 and BCT4, were selected according to its their growth inducing capacity. The BCT9 strain elicited the greatest increases in dry weight and primary root length when L. sativa seedlings were subjected to a 10-day experiment. Finally, because acetoin only stimulated root growth, we suggest that other volatiles could be responsible for the growth promotion of L. sativa. In conclusion, our results strongly suggest that bacteria volatiles can be used as growth-inducers as alternative or complementary strategies for application in horticulture species. Copyright © 2016 Elsevier GmbH. All rights reserved.

  13. Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity

    NARCIS (Netherlands)

    J.A.M. Dols (Joke); D. Molenaar (Douwe); van der Helm, J.J. (Jannie J.); Caspers, M.P.M. (Martien P.M.); Angelino-Bart, A.K. (Alie de Kat); F.H.J. Schuren (Frank); Speksnijder, A.G.C.L. (Adrianus G.C.L.); Westerhoff, H.V. (Hans V.); J.H. Richardus (Jan Hendrik); Boon, M.E. (Mathilde E.); G. Reid (Gregor); de Vries, H.J.C. (Henry J.C.); R. Kort (Remco)

    2016-01-01

    markdownabstract__Background:__ To date, women are most often diagnosed with bacterial vaginosis (BV) using microscopy based Nugent scoring or Amsel criteria. However, the accuracy is less than optimal. The aim of the present study was to confirm the identity of known BV-associated composition

  14. Diversity and distribution of culturable lactic acid bacterial species in Indonesian Sayur Asin

    OpenAIRE

    Mangunwardoyo, Wibowo; Abinawanto,; Salamah, Andi; Sukara, Endang; Sulistiani,; Dinoto, Achmad

    2016-01-01

    Background and Objectives: Lactic acid bacteria (LAB) play important roles in processing of Sayur Asin (spontaneously fermented mustard). Unfortunately, information about LAB in Indonesian Sayur Asin, prepared by traditional manufactures which is important as baseline data for maintenance of food quality and safety, is unclear. The aim of this study was to describe the diversity and distribution of culturable lactic acid bacteria in Sayur Asin of Indonesia.Materials and Methods: Four Sayur As...

  15. Species diversity modulates predation

    NARCIS (Netherlands)

    Kratina, P.; Vos, M.; Anholt, B.R.

    2007-01-01

    Predation occurs in a context defined by both prey and non-prey species. At present it is largely unknown how species diversity in general, and species that are not included in a predator's diet in particular, modify predator–prey interactions.Therefore we studied how both the density and diversity

  16. Bacterial Diversity across Individual Lichens▿ †

    Science.gov (United States)

    Mushegian, Alexandra A.; Peterson, Celeste N.; Baker, Christopher C. M.; Pringle, Anne

    2011-01-01

    Symbioses are unique habitats for bacteria. We surveyed the spatial diversity of bacterial communities across multiple individuals of closely related lichens using terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing. Centers of lichens house richer, more consistent assemblages than species-poor and compositionally disparate lichen edges, suggesting that ecological succession plays a role in structuring these communities. PMID:21531831

  17. Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum

    Directory of Open Access Journals (Sweden)

    Meng Dong

    2018-02-01

    Full Text Available Endophytic bacteria are nearly ubiquitously present in the internal tissues of plants, and some endophytes can promote plant growth. In this study, we sampled the roots of four ancestral species of sugarcane (two genotypes per species and two sugarcane cultivars, and used 16S rRNA and nifH gene sequencing to characterize the root endophytic bacterial communities and diazotroph diversity. A total of 7,198 operational taxonomic units (OTUs were detected for the endophytic bacteria community. The endophytic bacterial communities exhibited significantly different α- and β-diversities. From the 202 detected families in the sugarcane roots, a core microbiome containing 13 families was identified. The nifH gene was successfully detected in 9 of 30 samples from the four sugarcane species assayed, and 1,734 OTUs were merged for endophytic diazotrophs. In the tested samples, 43 families of endophytic diazotrophs were detected, and six families showed differences across samples. Among the 20 most abundant detected genera, 10 have been reported to be involved in nitrogen fixation in sugarcane. These findings demonstrate the diversity of the microbial communities in different sugarcane germplasms and shed light on the mechanism of biological nitrogen fixation in sugarcane.

  18. The Bacterial Species Campylobacter jejuni Induce Diverse Innate Immune Responses in Human and Avian Intestinal Epithelial Cells

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    Daniel A. John

    2017-09-01

    Full Text Available Campylobacter remain the major cause of human gastroenteritis in the Developed World causing a significant burden to health services. Campylobacter are pathogens in humans and chickens, although differences in mechanistic understanding are incomplete, in part because phenotypic strain diversity creates inconsistent findings. Here, we took Campylobacter jejuni isolates (n = 100 from multi-locus sequence typed collections to assess their pathogenic diversity, through their inflammatory, cytotoxicity, adhesion, invasion and signaling responses in a high-throughput model using avian and human intestinal epithelial cells. C. jejuni induced IL-8 and CXCLi1/2 in human and avian epithelial cells, respectively, in a MAP kinase-dependent manner. In contrast, IL-10 responses in both cell types were PI 3-kinase/Akt-dependent. C. jejuni strains showed diverse levels of invasion with high invasion dependent on MAP kinase signaling in both cell lines. C. jejuni induced diverse cytotoxic responses in both cell lines with cdt-positive isolates showing significantly higher toxicity. Blockade of endocytic pathways suggested that invasion by C. jejuni was clathrin- and dynamin-dependent but caveolae- independent in both cells. In contrast, IL-8 (and CXCLi1/2 production was dependent on clathrin, dynamin, and caveolae. This study is important because of its scale, and the data produced, suggesting that avian and human epithelial cells use similar innate immune pathways where the magnitude of the response is determined by the phenotypic diversity of the Campylobacter species.

  19. Leaf bacterial diversity mediates plant diversity and ecosystem function relationships.

    Science.gov (United States)

    Laforest-Lapointe, Isabelle; Paquette, Alain; Messier, Christian; Kembel, Steven W

    2017-06-01

    Research on biodiversity and ecosystem functioning has demonstrated links between plant diversity and ecosystem functions such as productivity. At other trophic levels, the plant microbiome has been shown to influence host plant fitness and function, and host-associated microbes have been proposed to influence ecosystem function through their role in defining the extended phenotype of host organisms However, the importance of the plant microbiome for ecosystem function has not been quantified in the context of the known importance of plant diversity and traits. Here, using a tree biodiversity-ecosystem functioning experiment, we provide strong support for the hypothesis that leaf bacterial diversity is positively linked to ecosystem productivity, even after accounting for the role of plant diversity. Our results also show that host species identity, functional identity and functional diversity are the main determinants of leaf bacterial community structure and diversity. Our study provides evidence of a positive correlation between plant-associated microbial diversity and terrestrial ecosystem productivity, and a new mechanism by which models of biodiversity-ecosystem functioning relationships can be improved.

  20. Balance of bacterial species in the gut

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Balance of bacterial species in the gut. Protective. Lactobacillus species. Bifidobacterium species. Selected E. coli. Saccharomyces boulardii. Clostridium butyricum.

  1. Prices and species diversity

    DEFF Research Database (Denmark)

    Sauer, Johannes

    of biodiversity and the appropriate incorporation in stochastic fron-tier models to achieve more realistic measures of production efficiency. We use the empirical example of tobacco production drawing from as well as affecting species diversity in the surrounding forests. We apply a shadow profit distance......In recent decades a significant amount of literature has been produced concerned with establishing a link between production efficiency and environmental efficiency with respect to quantitative modelling. This has been mainly addressed by focusing on the incorporation of undesirable outputs...... or the incorporation of environmentally det-rimental inputs. However, while the debate with respect to linear programming based DEA modelling is already at an advanced stage the corresponding one with respect to stochastic frontier modelling still needs considerable efforts. This contribution fo-cuses on the case...

  2. Benthic bacterial diversity in submerged sinkhole ecosystems.

    Science.gov (United States)

    Nold, Stephen C; Pangborn, Joseph B; Zajack, Heidi A; Kendall, Scott T; Rediske, Richard R; Biddanda, Bopaiah A

    2010-01-01

    Physicochemical characterization, automated ribosomal intergenic spacer analysis (ARISA) community profiling, and 16S rRNA gene sequencing approaches were used to study bacterial communities inhabiting submerged Lake Huron sinkholes inundated with hypoxic, sulfate-rich groundwater. Photosynthetic cyanobacterial mats on the sediment surface were dominated by Phormidium autumnale, while deeper, organically rich sediments contained diverse and active bacterial communities.

  3. Estimating bacterial diversity for ecological studies: methods, metrics, and assumptions.

    Directory of Open Access Journals (Sweden)

    Julia Birtel

    Full Text Available Methods to estimate microbial diversity have developed rapidly in an effort to understand the distribution and diversity of microorganisms in natural environments. For bacterial communities, the 16S rRNA gene is the phylogenetic marker gene of choice, but most studies select only a specific region of the 16S rRNA to estimate bacterial diversity. Whereas biases derived from from DNA extraction, primer choice and PCR amplification are well documented, we here address how the choice of variable region can influence a wide range of standard ecological metrics, such as species richness, phylogenetic diversity, β-diversity and rank-abundance distributions. We have used Illumina paired-end sequencing to estimate the bacterial diversity of 20 natural lakes across Switzerland derived from three trimmed variable 16S rRNA regions (V3, V4, V5. Species richness, phylogenetic diversity, community composition, β-diversity, and rank-abundance distributions differed significantly between 16S rRNA regions. Overall, patterns of diversity quantified by the V3 and V5 regions were more similar to one another than those assessed by the V4 region. Similar results were obtained when analyzing the datasets with different sequence similarity thresholds used during sequences clustering and when the same analysis was used on a reference dataset of sequences from the Greengenes database. In addition we also measured species richness from the same lake samples using ARISA Fingerprinting, but did not find a strong relationship between species richness estimated by Illumina and ARISA. We conclude that the selection of 16S rRNA region significantly influences the estimation of bacterial diversity and species distributions and that caution is warranted when comparing data from different variable regions as well as when using different sequencing techniques.

  4. Chapter 16: Species Diversity

    African Journals Online (AJOL)

    zargaran

    2012-05-03

    May 3, 2012 ... rarefaction method was recorded in Pardanan, with 28 oak gall wasps species. Furthermore, the highest amount of Gini-Simpson and Shannon entropy index were recorded in Sardasht, while the highest evenness was recorded in Shalmash. Differences in the local distribution of oak species, especially.

  5. Bacterial diversity at different stages of the composting process

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    Paulin Lars

    2010-03-01

    Full Text Available Abstract Background Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA. Results Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts. Conclusions Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants.

  6. Chamaedorea: diverse species in diverse habitats

    Directory of Open Access Journals (Sweden)

    1992-01-01

    Full Text Available DIVERSES ESPÈCES DANS DIVERS HABITATS. Des espèces extraordinairement diverses se trouvant dans des habitats également divers caractérisent Chamaedorea, un genre qui compte environ 90 espèces dioïques limitées aux sous-bois des forêts néo-tropicales constamment dans la pluie et les nuages du Mexique à la Bolivie et à l’Équateur. Une vaste gamme de formes biologiques, de tiges, de feuilles, d’inflorescences, de fleurs, et de fruits reflète la diversité des espèces. Bien que le genre soit plus riche en espèces dans les forêts denses et humides situées entre 800-1,500 mètres d’altitude, quelques espèces exceptionnelles se trouvent dans des forêts moins denses et/ou occasionnellement sèches, sur des substances dures ou dans d’autres habitats inhabituels. DIVERSAS ESPECIES EN DIVERSOS HÁBITATS. Especies notablemente diversas presentes en habitats igualmente diversos caracterizan a Chamaedorea, un genero de aproximadamente 90 especies dioicas limitadas al sotobosque de los bosques lluviosos y nubosos neotropicales desde Mexico hasta Bolivia y Ecuador. Una amplia gama de formas biológicas, tallos, hojas, inflorescencias, flores, y frutos refleja la diversidad de las especies. Aunque el género es más rico en especies en los bosques densos y húmedos de 800-1,500 metros de altura, unas pocas especies excepcionales ocurren en bosques abiertos o ocasionalmente secos, en substrato severo o en otros habitats extraordinarios. Remarkably diverse species occurring in equally diverse habitats characterize Chamaedorea, a genus of about 90, dioecious species restricted to the understory of neotropical rain and cloud forests from Mexico to Bolivia and Ecuador. A vast array of habits, stems, leaves, inflorescences, flowers, and fruits reflect the diversity of species. Although the genus is most species-rich in dense, moist or wet, diverse forests from 800-1,500 meters elevation, a few exceptional species occur in open and/or seasonally

  7. Prevalent Bacterial Species and Novel Phylotypes in Advanced Noma Lesions

    OpenAIRE

    Paster, B. J.; Falkler, Jr., W. A.; Enwonwu, C. O.; Idigbe, E. O.; Savage, K. O.; Levanos, V. A.; Tamer, M. A.; Ericson, R. L.; Lau, C. N.; Dewhirst, F. E.

    2002-01-01

    The purpose of this study was to determine the bacterial diversity in advanced noma lesions using culture-independent molecular methods. 16S ribosomal DNA bacterial genes from DNA isolated from advanced noma lesions of four Nigerian children were PCR amplified with universally conserved primers and spirochetal selective primers and cloned into Escherichia coli. Partial 16S rRNA sequences of approximately 500 bases from 212 cloned inserts were used initially to determine species identity or cl...

  8. Horizontal gene transfer and bacterial diversity

    Indian Academy of Sciences (India)

    Unknown

    This review discusses how the recent influx of complete chromosomal sequences of various ... enteric bacteria, a great deal of phenotypic diversity among species is ..... E V 1998 Evidence for massive gene exchange between archaeal and ...

  9. Diversity rankings among bacterial lineages in soil.

    Science.gov (United States)

    Youssef, Noha H; Elshahed, Mostafa S

    2009-03-01

    We used rarefaction curve analysis and diversity ordering-based approaches to rank the 11 most frequently encountered bacterial lineages in soil according to diversity in 5 previously reported 16S rRNA gene clone libraries derived from agricultural, undisturbed tall grass prairie and forest soils (n=26,140, 28 328, 31 818, 13 001 and 53 533). The Planctomycetes, Firmicutes and the delta-Proteobacteria were consistently ranked among the most diverse lineages in all data sets, whereas the Verrucomicrobia, Gemmatimonadetes and beta-Proteobacteria were consistently ranked among the least diverse. On the other hand, the rankings of alpha-Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes and Chloroflexi varied widely in different soil clone libraries. In general, lineages exhibiting largest differences in diversity rankings also exhibited the largest difference in relative abundance in the data sets examined. Within these lineages, a positive correlation between relative abundance and diversity was observed within the Acidobacteria, Actinobacteria and Chloroflexi, and a negative diversity-abundance correlation was observed within the Bacteroidetes. The ecological and evolutionary implications of these results are discussed.

  10. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny

    2006-01-01

    species present were identified. More than one bacterial species were detected in all the ulcers. The most common bacteria found were Staphylococcus aureus (found in 93.5% of the ulcers), Enterococcus faecalis (71.7%), Pseudomonas aeruginosa (52.2%), coagulase-negative staphylococci (45.7%), Proteus...

  11. Bacterial acquisition in juveniles of several broadcast spawning coral species.

    Directory of Open Access Journals (Sweden)

    Koty H Sharp

    Full Text Available Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals.

  12. Bacterial acquisition in juveniles of several broadcast spawning coral species.

    Science.gov (United States)

    Sharp, Koty H; Ritchie, Kim B; Schupp, Peter J; Ritson-Williams, Raphael; Paul, Valerie J

    2010-05-28

    Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH) using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals.

  13. Comparisons of host mitochondrial, nuclear and endosymbiont bacterial genes reveal cryptic fig wasp species and the effects of Wolbachia on host mtDNA evolution and diversity

    Directory of Open Access Journals (Sweden)

    Feng Gui

    2011-04-01

    Full Text Available Abstract Background Figs and fig-pollinating wasp species usually display a highly specific one-to-one association. However, more and more studies have revealed that the "one-to-one" rule has been broken. Co-pollinators have been reported, but we do not yet know how they evolve. They may evolve from insect speciation induced or facilitated by Wolbachia which can manipulate host reproduction and induce reproductive isolation. In addition, Wolbachia can affect host mitochondrial DNA evolution, because of the linkage between Wolbachia and associated mitochondrial haplotypes, and thus confound host phylogeny based on mtDNA. Previous research has shown that fig wasps have the highest incidence of Wolbachia infection in all insect taxa, and Wolbachia may have great influence on fig wasp biology. Therefore, we look forward to understanding the influence of Wolbachia on mitochondrial DNA evolution and speciation in fig wasps. Results We surveyed 76 pollinator wasp specimens from nine Ficus microcarpa trees each growing at a different location in Hainan and Fujian Provinces, China. We found that all wasps were morphologically identified as Eupristina verticillata, but diverged into three clades with 4.22-5.28% mtDNA divergence and 2.29-20.72% nuclear gene divergence. We also found very strong concordance between E. verticillata clades and Wolbachia infection status, and the predicted effects of Wolbachia on both mtDNA diversity and evolution by decreasing mitochondrial haplotypes. Conclusions Our study reveals that the pollinating wasp E. verticillata on F. microcarpa has diverged into three cryptic species, and Wolbachia may have a role in this divergence. The results also indicate that Wolbachia strains infecting E. verticillata have likely resulted in selective sweeps on host mitochondrial DNA.

  14. Assessment of bacterial diversity during composting of agricultural byproducts

    Science.gov (United States)

    2013-01-01

    Background Composting is microbial decomposition of biodegradable materials and it is governed by physicochemical, physiological and microbiological factors. The importance of microbial communities (bacteria, actinomycetes and fungi) during composting is well established. However, the microbial diversity during composting may vary with the variety of composting materials and nutrient supplements. Therefore, it is necessary to study the diversity of microorganisms during composting of different agricultural byproducts like wheat bran, rice bran, rice husk, along with grass clippings and bulking agents. Here it has been attempted to assess the diversity of culturable bacteria during composting of agricultural byproducts. Results The culturable bacterial diversity was assessed during the process by isolating the most prominent bacteria. Bacterial population was found to be maximum during the mesophilic phase, but decreased during the thermophilic phase and declined further in the cooling and maturation phase of composting. The bacterial population ranged from 105 to 109 cfu g-1 compost. The predominant bacteria were characterized biochemically, followed by 16S rRNA gene sequencing. The isolated strains, both Gram-positive and Gram-negative groups belonged to the order Burkholderiales, Enterobacteriales, Actinobacteriales and Bacillales, which includes genera e.g. Staphylococcus, Serratia, Klebsiella, Enterobacter, Terribacillus, Lysinibacillus Kocuria, Microbacterium, Acidovorax and Comamonas. Genera like Kocuria, Microbacterium, Acidovorax, Comamonas and some new species of Bacillus were also identified for the first time from the compost made from agricultural byproducts. Conclusion The use of appropriate nitrogen amendments and bulking agents in composting resulted in good quality compost. The culture based strategy enabled us to isolate some novel bacterial isolates like Kocuria, Microbacterium, Acidovorax and Comamonas first time from agro-byproducts compost

  15. Panamanian frog species host unique skin bacterial communities

    Directory of Open Access Journals (Sweden)

    Lisa K. Belden

    2015-10-01

    Full Text Available Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd, that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26% were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in

  16. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny

    2006-01-01

    . aeruginosa were found to be significantly larger than ulcers without the presence of P. aeruginosa (P wound is colonised by multiple bacterial species and that once they are established many of them persist in the wound. Our results suggest that the presence...... of P. aeruginosa in venous leg ulcers can induce ulcer enlargement and/or cause delayed healing....

  17. Prevalent bacterial species and novel phylotypes in advanced noma lesions.

    Science.gov (United States)

    Paster, B J; Falkler Jr, W A; Enwonwu, C O; Idigbe, E O; Savage, K O; Levanos, V A; Tamer, M A; Ericson, R L; Lau, C N; Dewhirst, F E

    2002-06-01

    The purpose of this study was to determine the bacterial diversity in advanced noma lesions using culture-independent molecular methods. 16S ribosomal DNA bacterial genes from DNA isolated from advanced noma lesions of four Nigerian children were PCR amplified with universally conserved primers and spirochetal selective primers and cloned into Escherichia coli. Partial 16S rRNA sequences of approximately 500 bases from 212 cloned inserts were used initially to determine species identity or closest relatives by comparison with sequences of known species or phylotypes. Nearly complete sequences of approximately 1,500 bases were obtained for most of the potentially novel species. A total of 67 bacterial species or phylotypes were detected, 25 of which have not yet been grown in vitro. Nineteen of the species or phylotypes, including Propionibacterium acnes, Staphylococcus spp., and the opportunistic pathogens Stenotrophomonas maltophilia and Ochrobactrum anthropi were detected in more than one subject. Other known species that were detected included Achromobacter spp., Afipia spp., Brevundimonas diminuta, Capnocytophaga spp., Cardiobacterium sp., Eikenella corrodens, Fusobacterium spp., Gemella haemoylsans, and Neisseria spp. Phylotypes that were unique to noma infections included those in the genera Eubacterium, Flavobacterium, Kocuria, Microbacterium, and Porphyromonas and the related Streptococcus salivarius and genera Sphingomonas and TREPONEMA: Since advanced noma lesions are infections open to the environment, it was not surprising to detect species not commonly associated with the oral cavity, e.g., from soil. Several species previously implicated as putative pathogens of noma, such as spirochetes and Fusobacterium spp., were detected in at least one subject. However, due to the limited number of available noma subjects, it was not possible at this time to associate specific species with the disease.

  18. Changes of Bacterial Diversity Depend on the Spoilage of Fresh Vegetables

    Directory of Open Access Journals (Sweden)

    Dong Hwan Lee

    2011-04-01

    Full Text Available Almost 10~30% of vegetables were discarded by the spoilage from farms to tables. After harvest, vegetables are often spoiled by a wide variety of microorganisms including many bacterial and fungal species. This investigation was conducted to extent the knowledge of relationship the spoilage of vegetables and the diversity of microbes. The total aerobic bacterial numbers in fresh lettuce, perilla leaf, and chicory were 2.6~2.7×106, 4.6×105, 1.2×106 CFU/g of fresh weight, respectively. The most common bacterial species were Pseudomonas spp., Alysiella spp., and Burkholderia spp., and other 18 more genera were involved in. After one week of incubation of those vegetables at 28℃, the microbial diversity had been changed. The total aerobic bacterial numbers increased to 1.1~4.6×108, 4.9×107, and 7.6×108 CFU/g of fresh weight for lettuce, perilla leaf, and chicory that is about 102 times increased bacterial numbers than that before spoilage. However, the diversity of microbes isolated had been simplified and fewer bacterial species had been isolated. The most bacterial population (~48% was taken up by Pseudomonas spp., and followed by Arthrobacter spp. and Bacillus spp. The spoilage activity of individual bacterial isolates had been tested using axenic lettuce plants. Among tested isolates, Pseudomonas fluorescence and Pantoea agglomerans caused severe spoilage on lettuce.

  19. Bacterial Diversity in the Digestive Tracts of Four Indian Air-Breathing Fish Species Investigated by PCR Based Denaturing Gradient Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Suxu He

    Full Text Available ABSTRACT An investigation was conducted to identify the allochthonous microbiota (entire intestine and the autochthonous microbiota in proximal intestine (PI and distal intestine (DI of four species of Indian air-breathing fish (climbing perch; Anabas testudineus, murrel; Channa punctatus, walking catfish; Clarias batrachus and stinging catfish; Heteropneustes fossilis by PCR based denaturing gradient gel electrophoresis (DGGE. High similarities of the allochthonous microbiota were observed between climbing perch and murrel, walking catfish and stinging catfish, indicating similar food behavior. The autochthonous microbiota of PI and DI from climbing perch and murrel revealed more similarity, than the result obtained from walking catfish and stinging catfish. The autochthonous microbiota of climbing perch and murrel were similar with regard to the allochthonous microbiota, but no such similarity was observed in case of walking catfish and stinging catfish. The fish genotype and intestinal bacteria are well matched and show co-evolutionary relationship. Three fish species has its unique bacteria; autochthonous Enterobacter cloacae, Edwardsiella tarda and Sphingobium sp. in DI of climbing perch, Pseudomonas sp.; allochthonous and autochthonous in PI of walking catfish and uncultured bacterium (EU697160.1, uncultured bacterium (JF018065.1 and uncultured bacterium (EU697160.1 for stinging catfish. In murrel, no unique bacteria were detected.

  20. Recombination-Driven Genome Evolution and Stability of Bacterial Species.

    Science.gov (United States)

    Dixit, Purushottam D; Pang, Tin Yau; Maslov, Sergei

    2017-09-01

    While bacteria divide clonally, horizontal gene transfer followed by homologous recombination is now recognized as an important contributor to their evolution. However, the details of how the competition between clonality and recombination shapes genome diversity remains poorly understood. Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. In the divergent regime, characterized by either a low recombination frequency or strict barriers to recombination, cohesion due to recombination is not sufficient to overcome the mutational drift. As a consequence, the divergence between pairs of genomes in the population steadily increases in the course of their evolution. The species lacks genetic coherence with sexually isolated clonal subpopulations continuously formed and dissolved. In contrast, in the metastable regime, characterized by a high recombination frequency combined with low barriers to recombination, genomes continuously recombine with the rest of the population. The population remains genetically cohesive and temporally stable. Notably, the transition between these two regimes can be affected by relatively small changes in evolutionary parameters. Using the Multi Locus Sequence Typing (MLST) data, we classify a number of bacterial species to be either the divergent or the metastable type. Generalizations of our framework to include selection, ecologically structured populations, and horizontal gene transfer of nonhomologous regions are discussed as well. Copyright © 2017 by the Genetics Society of America.

  1. Spatial patterns of species diversity in Kenya

    NARCIS (Netherlands)

    Oindo, B.O.

    2001-01-01

    The most striking feature of Earth is the existence of life and the most striking feature of life is its diversity. Explaining patterns of species diversity is one of the most complex problems in ecology. This is because diversity is usually the outcome of many contributing factors whose relative

  2. Species Diversity Enhances Predator Growth Rates

    International Nuclear Information System (INIS)

    Olson, M.H.; Jacobs, R.P.; O'Donnell, E.B.

    2007-01-01

    Predators can be important top-down regulators of community structure and are known to have both positive and negative effects on species diversity. However, little is known about the reciprocal effects of species diversity on predators. Across a set of 80 lakes in Connecticut, USA, we found a strong positive correlation between prey species diversity (using the Shannon-Weiner Diversity Index) and growth rates of largemouth bass (Micropterus salmoides). This correlation was strongest for small predators and decreased with body size. Although the underlying mechanisms are not known, the correlation is not driven by total fish abundance, predator abundance, or productivity.

  3. Benthic Bacterial Diversity in Submerged Sinkhole Ecosystems▿ †

    Science.gov (United States)

    Nold, Stephen C.; Pangborn, Joseph B.; Zajack, Heidi A.; Kendall, Scott T.; Rediske, Richard R.; Biddanda, Bopaiah A.

    2010-01-01

    Physicochemical characterization, automated ribosomal intergenic spacer analysis (ARISA) community profiling, and 16S rRNA gene sequencing approaches were used to study bacterial communities inhabiting submerged Lake Huron sinkholes inundated with hypoxic, sulfate-rich groundwater. Photosynthetic cyanobacterial mats on the sediment surface were dominated by Phormidium autumnale, while deeper, organically rich sediments contained diverse and active bacterial communities. PMID:19880643

  4. In search of a bacterial species definition

    Directory of Open Access Journals (Sweden)

    Edgardo Moreno

    2002-06-01

    Full Text Available Abstract: The bacterial species concept was examined within the framework of plant and animal associated α-2 proteobacteria, taking into consideration the phylogenetic, taxonomic and biological approaches as well as the microbiologists perception. The virtue of the phylogenetic approach is that it gives an evolutionary perspective of the bacterial lineage; however the methods used possess low resolution for defining species located at the terminal branches of the phylogenetic trees. The merit of the taxonomic approach is that species are defined on the basis of multiple characteristics allowing high resolution at the terminal branches of dendograms; its disadvantage is the inaccuracy in the earlier nodes. On an individual level, the qualitative biological characteristics used for the definition of species frequently reveal shortcomings because many of these properties are the result of coevolution, parallel evolution or the horizontal transfer of genes. Nevertheless, when considered together with !be phylogenetic and taxonomic approaches, important uncertainties are discovered: these must be weighed if a practical definition of bacterial species is conceived. The microbiologists' perception is !be criterion expressed by a group of sponsors who, based on scientific and practical grounds, propose a new bacterial species. The success of this new proposal is measured by its widespread acceptance and its permanence. A difficult problem concerned with defining bacterial species is how to distinguish if they are independent evolutionary units or if they are reticulate evolutionary units. In the first case the inherence is vertically transmitted as a result of binary fission and clonal expansion. This may be !be case of some animal cell associated bacteria in which recombination appears to be precluded or exceptional. In the second case adaptive changes occurring within an individual can be horizontaIly transferred to many or all group members. This

  5. Risk Assessment and effect of Penicillin-G on bacterial diversity in drinking water

    Science.gov (United States)

    Wu, Qing; Zhao, Xiaofei; Peng, Sen; Wang, Lei; Zhao, Xinhua

    2018-02-01

    Penicillin-G was detected in drinking water by LC-MS/MS and the bacterial diversity was investigated by PCR and high-throughput sequencing. The results showed that bacteria community structure in drinking water has undergone major changes when added different concentrations of penicillin-G. The diversity index of each sample was calculated. The results showed that the total number and abundance of bacterial community species in drinking water samples decreased significantly after the addition of penicillin-G. However, the number and abundance of community structure did not change with the concentration. Penicillin-G inhibits the activity of bacterial community in drinking water and can reduce the bacterial diversity in drinking water.

  6. Phenotypic and genetic diversity of the species Lactobacillus rhamnosus

    OpenAIRE

    Ceapa, C.D.

    2016-01-01

    The thesis explores the diversity of Lactobacillus rhamnosus, a species from which strains are studied for their anti-inflammatory, anti-allergic, and diarrhea preventing effects. The work combines observations on the behavior of the bacteria in a simplified laboratory setting (use of carbohydrates, immune modulation effects, anti-pathogenic effects) with genomic information obtained by sequencing, with the aim to pinpoint genes that could be relevant for bacterial survival and metabolic capa...

  7. Island Species Richness Increases with Habitat Diversity

    NARCIS (Netherlands)

    Hortal, J.; Triantis, K.A.; Meiri, S.; Thebault, E.M.C.; Sfenthourakis, S.

    2009-01-01

    Species richness is commonly thought to increase with habitat diversity. However, a recent theoretical model aiming to unify niche and island biogeography theories predicted a hump-shaped relationship between richness and habitat diversity. Given the contradiction between model results and previous

  8. Bacterial profile of dentine caries and the impact of pH on bacterial population diversity.

    Directory of Open Access Journals (Sweden)

    Nima Kianoush

    Full Text Available Dental caries is caused by the release of organic acids from fermentative bacteria, which results in the dissolution of hydroxyapatite matrices of enamel and dentine. While low environmental pH is proposed to cause a shift in the consortium of oral bacteria, favouring the development of caries, the impact of this variable has been overlooked in microbial population studies. This study aimed to detail the zonal composition of the microbiota associated with carious dentine lesions with reference to pH. We used 454 sequencing of the 16S rRNA gene (V3-V4 region to compare microbial communities in layers ranging in pH from 4.5-7.8 from 25 teeth with advanced dentine caries. Pyrosequencing of the amplicons yielded 449,762 sequences. Nine phyla, 97 genera and 409 species were identified from the quality-filtered, de-noised and chimera-free sequences. Among the microbiota associated with dentinal caries, the most abundant taxa included Lactobacillus sp., Prevotella sp., Atopobium sp., Olsenella sp. and Actinomyces sp. We found a disparity between microbial communities localised at acidic versus neutral pH strata. Acidic conditions were associated with low diversity microbial populations, with Lactobacillus species including L. fermentum, L. rhamnosus and L. crispatus, being prominent. In comparison, the distinctive species of a more diverse flora associated with neutral pH regions of carious lesions included Alloprevotella tanerrae, Leptothrix sp., Sphingomonas sp. and Streptococcus anginosus. While certain bacteria were affected by the pH gradient, we also found that ∼ 60% of the taxa associated with caries were present across the investigated pH range, representing a substantial core. We demonstrated that some bacterial species implicated in caries progression show selective clustering with respect to pH gradient, providing a basis for specific therapeutic strategies.

  9. Kisameet Glacial Clay: an Unexpected Source of Bacterial Diversity.

    Science.gov (United States)

    Svensson, Sarah L; Behroozian, Shekooh; Xu, Wanjing; Surette, Michael G; Li, Loretta; Davies, Julian

    2017-05-23

    Widespread antibiotic resistance among bacterial pathogens is providing the impetus to explore novel sources of antimicrobial agents. Recently, the potent antibacterial activity of certain clay minerals has stimulated scientific interest in these materials. One such example is Kisameet glacial clay (KC), an antibacterial clay from a deposit on the central coast of British Columbia, Canada. However, our understanding of the active principles of these complex natural substances is incomplete. Like soils, clays may possess complex mixtures of bacterial taxa, including the Actinobacteria , a clade known to be rich in antibiotic-producing organisms. Here, we present the first characterization of both the microbial and geochemical characteristics of a glacial clay deposit. KC harbors surprising bacterial species richness, with at least three distinct community types. We show that the deposit has clines of inorganic elements that can be leached by pH, which may be drivers of community structure. We also note the prevalence of Gallionellaceae in samples recovered near the surface, as well as taxa that include medically or economically important bacteria such as Actinomycetes and Paenibacillus These results provide insight into the microbial taxa that may be the source of KC antibacterial activity and suggest that natural clays may be rich sources of microbial and molecular diversity. IMPORTANCE Identifying and characterizing the resident microbial populations (bacteria, viruses, protozoa, and fungi) is key to understanding the ecology, chemistry, and homeostasis of virtually all sites on Earth. The Kisameet Bay deposit in British Columbia, Canada, holds a novel glacial clay with a history of medicinal use by local indigenous people. We previously showed that it has potent activity against a variety of antibiotic-resistant bacteria, suggesting it could complement our dwindling arsenal of antibiotics. Here, we have characterized the microbiome of this deposit to gain insight

  10. Bacterial diversity among four healthcare-associated institutes in Taiwan.

    Science.gov (United States)

    Chen, Chang-Hua; Lin, Yaw-Ling; Chen, Kuan-Hsueh; Chen, Wen-Pei; Chen, Zhao-Feng; Kuo, Han-Yueh; Hung, Hsueh-Fen; Tang, Chuan Yi; Liou, Ming-Li

    2017-08-15

    Indoor microbial communities have important implications for human health, especially in health-care institutes (HCIs). The factors that determine the diversity and composition of microbiomes in a built environment remain unclear. Herein, we used 16S rRNA amplicon sequencing to investigate the relationships between building attributes and surface bacterial communities among four HCIs located in three buildings. We examined the surface bacterial communities and environmental parameters in the buildings supplied with different ventilation types and compared the results using a Dirichlet multinomial mixture (DMM)-based approach. A total of 203 samples from the four HCIs were analyzed. Four bacterial communities were grouped using the DMM-based approach, which were highly similar to those in the 4 HCIs. The α-diversity and β-diversity in the naturally ventilated building were different from the conditioner-ventilated building. The bacterial source composition varied across each building. Nine genera were found as the core microbiota shared by all the areas, of which Acinetobacter, Enterobacter, Pseudomonas, and Staphylococcus are regarded as healthcare-associated pathogens (HAPs). The observed relationship between environmental parameters such as core microbiota and surface bacterial diversity suggests that we might manage indoor environments by creating new sanitation protocols, adjusting the ventilation design, and further understanding the transmission routes of HAPs.

  11. Species diversity of Trichoderma in Poland

    Science.gov (United States)

    Fifteen species of Trichoderma were identified from among 118 strains originating from different regions and ecological niches in Poland. This low number indicates low species diversity of Trichoderma in this Central European region. Using the ITS1-ITS2 regions, 64 strains were positively identified...

  12. Patterns of gut bacterial colonization in three primate species.

    Directory of Open Access Journals (Sweden)

    Erin A McKenney

    Full Text Available Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes. Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.

  13. Do species conservation assessments capture genetic diversity?

    Directory of Open Access Journals (Sweden)

    Malin C. Rivers

    2014-12-01

    Full Text Available The best known system for classifying threat status of species, the IUCN Red List, currently lacks explicit considerations of genetic diversity, and consequently may not account for potential adaptation of species to future environmental change. To address this gap, we integrate range-wide genetic analysis with IUCN Red List assessments.We calculated the loss of genetic diversity under simulated range loss for species of Delonix (Leguminosae. Simulated range loss involved random loss of populations and was intended to model ongoing habitat destruction. We found a strong relationship between loss of genetic diversity and range. Moreover, we found correspondence between levels of genetic diversity and thresholds for ‘non-threatened’ versus ‘threatened’ IUCN Red List categories.Our results support the view that current threat thresholds of the IUCN Red List criteria reflect genetic diversity, and hence evolutionary potential; although the genetic diversity distinction between threatened categories was less evident. Thus, by supplementing conventional conservation assessments with genetic data, new insights into the biological robustness of IUCN Red List assessments for targeted conservation initiatives can be achieved. Keywords: Conservation assessment, Conservation genetics, Extinction risk, Genetic diversity, IUCN Red List, Range

  14. SPECIES DIVERSITY AND STABILITY OF BIRD COMMUNITIES

    Directory of Open Access Journals (Sweden)

    Matsyura M.V.

    2011-12-01

    Full Text Available When comparing the suggested stability indicators, we obtained statistically significant correlations for indicators of annual stability of species and total number and standard deviation of the logarithm of the number. Annual Stability Index can be applied with a high degree of reliability as a characteristic of the averaged structure of the community and its pyramid of abundances. The results of correlation analysis confirm our assumptions about the correlation between stability over the years and indices of species diversity and relative uniformity.The final task of the study was to create a mathematical model of stability, where the independent variables are the indices of species diversity. The calculation of these indices allows forecasting birds’ community stability. According to the result of multiple regression for the indicators of diversity and stability of the breeding birds’ community highest correlation coefficients were obtained fro Shannon index and Simpson's dominance Index.Community stability could be determined by its overall species diversity. When considering the stability of community its diversity should be considered as a combination of uniformity of their total number and number of species. The most suitable predictors for the community stability were the nonparametric index of dominance and information-statistical indices, since they considered simultaneously evenness and richness. The community stability is subject of the complexity of its internal communications pattern.

  15. New insights into valve-related intramural and intracellular bacterial diversity in infective endocarditis.

    Science.gov (United States)

    Oberbach, Andreas; Schlichting, Nadine; Feder, Stefan; Lehmann, Stefanie; Kullnick, Yvonne; Buschmann, Tilo; Blumert, Conny; Horn, Friedemann; Neuhaus, Jochen; Neujahr, Ralph; Bagaev, Erik; Hagl, Christian; Pichlmaier, Maximilian; Rodloff, Arne Christian; Gräber, Sandra; Kirsch, Katharina; Sandri, Marcus; Kumbhari, Vivek; Behzadi, Armirhossein; Behzadi, Amirali; Correia, Joao Carlos; Mohr, Friedrich Wilhelm; Friedrich, Maik

    2017-01-01

    In infective endocarditis (IE), a severe inflammatory disease of the endocardium with an unchanged incidence and mortality rate over the past decades, only 1% of the cases have been described as polymicrobial infections based on microbiological approaches. The aim of this study was to identify potential biodiversity of bacterial species from infected native and prosthetic valves. Furthermore, we compared the ultrastructural micro-environments to detect the localization and distribution patterns of pathogens in IE. Using next-generation sequencing (NGS) of 16S rDNA, which allows analysis of the entire bacterial community within a single sample, we investigated the biodiversity of infectious bacterial species from resected native and prosthetic valves in a clinical cohort of 8 IE patients. Furthermore, we investigated the ultrastructural infected valve micro-environment by focused ion beam scanning electron microscopy (FIB-SEM). Biodiversity was detected in 7 of 8 resected heart valves. This comprised 13 bacterial genera and 16 species. In addition to 11 pathogens already described as being IE related, 5 bacterial species were identified as having a novel association. In contrast, valve and blood culture-based diagnosis revealed only 4 species from 3 bacterial genera and did not show any relevant antibiotic resistance. The antibiotics chosen on this basis for treatment, however, did not cover the bacterial spectra identified by our amplicon sequencing analysis in 4 of 8 cases. In addition to intramural distribution patterns of infective bacteria, intracellular localization with evidence of bacterial immune escape mechanisms was identified. The high frequency of polymicrobial infections, pathogen diversity, and intracellular persistence of common IE-causing bacteria may provide clues to help explain the persistent and devastating mortality rate observed for IE. Improved bacterial diagnosis by 16S rDNA NGS that increases the ability to tailor antibiotic therapy may

  16. Region effects influence local tree species diversity.

    Science.gov (United States)

    Ricklefs, Robert E; He, Fangliang

    2016-01-19

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species.

  17. Physio-chemical characteristics and bacterial diversity in copper ...

    African Journals Online (AJOL)

    The effects of seasonal change in temperature on the chemical compositions of water and bacterial diversity in copper mining wastewater reservoir (CMWR) located in Jiangxi province, China, was investigated. Wastewater samples were collected collected in December 2008 and May 2009 from different points of CMWR ...

  18. Metagenomic analysis of bacterial diversity of Siloam hot water ...

    African Journals Online (AJOL)

    The bacterial diversity of Siloam hot water spring was determined using 454 pyrosequencing of two 16S rRNA variable regions V1-3 and V4-7. Analysis of the community DNA revealed that the phyla Proteobacteria, Cyanobacteria, Bacteriodetes, Planctomycetes, Firmicutes, Chloroflexi and Verrucomicrobia were the most ...

  19. Analysis of the Bacterial Diversity in Liver Abscess: Differences between Pyogenic and Amebic Abscesses

    Science.gov (United States)

    Reyna-Fabián, Miriam E.; Zermeño, Valeria; Ximénez, Cecilia; Flores, Janin; Romero, Miguel F.; Diaz, Daniel; Argueta, Jesús; Moran, Patricia; Valadez, Alicia; Cerritos, René

    2016-01-01

    Several recent studies have demonstrated that virulence in Entamoeba histolytica is triggered in the presence of both pathogenic and nonpathogenic bacteria species using in vitro and in vivo experimental animal models. In this study, we examined samples aspirated from abscess material obtained from patients who were clinically diagnosed with amebic liver abscess (ALA) or pyogenic liver abscess (PLA). To determine the diversity of bacterial species in the abscesses, we performed partial 16S rRNA gene sequencing. In addition, the E. histolytica and Entamoeba dispar species were genotyped using tRNA-linked short tandem repeats as specific molecular markers. The association between clinical data and bacterial and parasite genotypes were examined through a correspondence analysis. The results showed the presence of numerous bacterial groups. These taxonomic groups constitute common members of the gut microbiota, although all of the detected bacterial species have a close phylogenetic relationship with bacterial pathogens. Furthermore, some patients clinically diagnosed with PLA and ALA were coinfected with E. dispar or E. histolytica, which suggests that the virulence of these parasites increased in the presence of bacteria. However, no specific bacterial groups were associated with this effect. Together, our results suggest a nonspecific mechanism of virulence modulation by bacteria in Entamoeba. PMID:26572872

  20. It's all relative: ranking the diversity of aquatic bacterial communities.

    Science.gov (United States)

    Shaw, Allison K; Halpern, Aaron L; Beeson, Karen; Tran, Bao; Venter, J Craig; Martiny, Jennifer B H

    2008-09-01

    The study of microbial diversity patterns is hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. For many questions about richness and evenness, however, one only needs to know the relative order of diversity among samples rather than total diversity. We used 16S libraries from the Global Ocean Survey to investigate the ability of 10 diversity statistics (including rarefaction, non-parametric, parametric, curve extrapolation and diversity indices) to assess the relative diversity of six aquatic bacterial communities. Overall, we found that the statistics yielded remarkably similar rankings of the samples for a given sequence similarity cut-off. This correspondence, despite the different underlying assumptions of the statistics, suggests that diversity statistics are a useful tool for ranking samples of microbial diversity. In addition, sequence similarity cut-off influenced the diversity ranking of the samples, demonstrating that diversity statistics can also be used to detect differences in phylogenetic structure among microbial communities. Finally, a subsampling analysis suggests that further sequencing from these particular clone libraries would not have substantially changed the richness rankings of the samples.

  1. Bacterial diversity in permanently cold and alkaline ikaite columns from Greenland.

    Science.gov (United States)

    Schmidt, Mariane; Priemé, Anders; Stougaard, Peter

    2006-12-01

    Bacterial diversity in alkaline (pH 10.4) and permanently cold (4 degrees C) ikaite tufa columns from the Ikka Fjord, SW Greenland, was investigated using growth characterization of cultured bacterial isolates with Terminal-restriction fragment length polymorphism (T-RFLP) and sequence analysis of bacterial 16S rRNA gene fragments. More than 200 bacterial isolates were characterized with respect to pH and temperature tolerance, and it was shown that the majority were cold-active alkaliphiles. T-RFLP analysis revealed distinct bacterial communities in different fractions of three ikaite columns, and, along with sequence analysis, it showed the presence of rich and diverse bacterial communities. Rarefaction analysis showed that the 109 sequenced clones in the 16S rRNA gene library represented between 25 and 65% of the predicted species richness in the three ikaite columns investigated. Phylogenetic analysis of the 16S rRNA gene sequences revealed many sequences with similarity to alkaliphilic or psychrophilic bacteria, and showed that 33% of the cloned sequences and 33% of the cultured bacteria showed less than 97% sequence identity to known sequences in databases, and may therefore represent yet unknown species.

  2. Bacterial diversity in the foreland of the Tianshan No. 1 glacier, China

    International Nuclear Information System (INIS)

    Wu Xiukun; Zhang Wei; Liu Guangxiu; Zhang Gaosen; Yang Xuan; Hu Ping; Chen Tuo; Li Zhongqin

    2012-01-01

    There is compelling evidence that glaciers are retreating in many mountainous areas of the world due to global warming. With this glacier retreat, new habitats are being exposed that are colonized by microorganisms whose diversity and function are less well studied. Here, we characterized bacterial diversity along the chronosequences of the glacier No. 1 foreland that follows glacier retreat. An average of 10 000 sequences was obtained from each sample by 454 pyrosequencing. Using non-parametric and rarefaction estimated analysis, we found bacterial phylotype richness was high. The bacterial species turnover rate was especially high between sites exposed for 6 and 10 yr. Pyrosequencing showed tremendous bacterial diversity, among which the Acidobacteria, Actinobacteria, Bacteroidetes and Proteobacteria were found to be present at larger numbers at the study area. Meanwhile, the proportion of Bacteroidetes and Proteobacteria decreased and the proportion of Acidobacteria increased along the chronosequences. Some known functional bacterial genera were also detected and the sulfur- and sulfate-reducing bacteria were present in a lower proportion of sequences. These findings suggest that high-throughput pyrosequencing can comprehensively detect bacteria in the foreland, including rare groups, and give a deeper understanding of the bacterial community structure and variation along the chronosequences. (letter)

  3. Bacterial diversity in the foreland of the Tianshan No. 1 glacier, China

    Energy Technology Data Exchange (ETDEWEB)

    Xiukun, Wu; Wei, Zhang; Guangxiu, Liu; Gaosen, Zhang [Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou (China); Xuan, Yang; Ping, Hu [School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou (China); Tuo, Chen; Li Zhongqin, E-mail: liugx@lzb.ac.cn [State Key Laboratory of Cryospheric Sciences, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou (China)

    2012-03-15

    There is compelling evidence that glaciers are retreating in many mountainous areas of the world due to global warming. With this glacier retreat, new habitats are being exposed that are colonized by microorganisms whose diversity and function are less well studied. Here, we characterized bacterial diversity along the chronosequences of the glacier No. 1 foreland that follows glacier retreat. An average of 10 000 sequences was obtained from each sample by 454 pyrosequencing. Using non-parametric and rarefaction estimated analysis, we found bacterial phylotype richness was high. The bacterial species turnover rate was especially high between sites exposed for 6 and 10 yr. Pyrosequencing showed tremendous bacterial diversity, among which the Acidobacteria, Actinobacteria, Bacteroidetes and Proteobacteria were found to be present at larger numbers at the study area. Meanwhile, the proportion of Bacteroidetes and Proteobacteria decreased and the proportion of Acidobacteria increased along the chronosequences. Some known functional bacterial genera were also detected and the sulfur- and sulfate-reducing bacteria were present in a lower proportion of sequences. These findings suggest that high-throughput pyrosequencing can comprehensively detect bacteria in the foreland, including rare groups, and give a deeper understanding of the bacterial community structure and variation along the chronosequences. (letter)

  4. Relationship between bacterial diversity and environmental parameters during composting of different raw materials.

    Science.gov (United States)

    Wang, Xueqin; Cui, Hongyang; Shi, Jianhong; Zhao, Xinyu; Zhao, Yue; Wei, Zimin

    2015-12-01

    The aim of this study was to compare the bacterial structure of seven different composts. The primary environmental factors affecting bacterial species were identified, and a strategy to enhance the abundance of uncultured bacteria through controlling relevant environmental parameters was proposed. The results showed that the physical-chemical parameters of each different pile changed in its own manner during composting, which affected the structure and succession of bacteria in different ways. DGGE profiles showed that there were 10 prominent species during composting. Among them, four species existed in all compost types, two species existed in several piles and four species were detected in a single material. Redundancy analysis results showed that bacterial species compositions were significantly influenced by C/N and moisture (p<0.05). The optimal range of C/N was 14-27. Based on these results, the primary environmental factors affecting a certain species were further identified as a potential control of bacterial diversity. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Bacterial diversity characterization in petroleum samples from Brazilian reservoirs

    Science.gov (United States)

    de Oliveira, Valéria Maia; Sette, Lara Durães; Simioni, Karen Christina Marques; dos Santos Neto, Eugênio Vaz

    2008-01-01

    This study aimed at evaluating potential differences among the bacterial communities from formation water and oil samples originated from biodegraded and non-biodegraded Brazilian petroleum reservoirs by using a PCR-DGGE based approach. Environmental DNA was isolated and used in PCR reactions with bacterial primers, followed by separation of 16S rDNA fragments in the DGGE. PCR products were also cloned and sequenced, aiming at the taxonomic affiliation of the community members. The fingerprints obtained allowed the direct comparison among the bacterial communities from oil samples presenting distinct degrees of biodegradation, as well as between the communities of formation water and oil sample from the non-biodegraded reservoir. Very similar DGGE band profiles were observed for all samples, and the diversity of the predominant bacterial phylotypes was shown to be low. Cloning and sequencing results revealed major differences between formation water and oil samples from the non-biodegraded reservoir. Bacillus sp. and Halanaerobium sp. were shown to be the predominant components of the bacterial community from the formation water sample, whereas the oil sample also included Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. and Acidithiobacillus ferrooxidans. The PCR-DGGE technique, combined with cloning and sequencing of PCR products, revealed the presence of taxonomic groups not found previously in these samples when using cultivation-based methods and 16S rRNA gene library assembly, confirming the need of a polyphasic study in order to improve the knowledge of the extent of microbial diversity in such extreme environments. PMID:24031244

  6. Bacterial biomass and DNA diversity in an alluvial meadow soil upon long-term fertilization

    NARCIS (Netherlands)

    Naumova, N.B.; Kuikman, P.J.

    2001-01-01

    The denaturing gradient gel-electrophoresis of bacterial DNA fragments and the assessment of bacterial biomass revealed changes in the diversity of the bacterial community in a meadow alluvial soil upon long-term fertilization.

  7. Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape.

    Directory of Open Access Journals (Sweden)

    Lucie Zinger

    2011-05-01

    Full Text Available The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution.Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity.Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.

  8. Bacterial diversity in two Neonatal Intensive Care Units (NICUs.

    Directory of Open Access Journals (Sweden)

    Krissi M Hewitt

    Full Text Available Infants in Neonatal Intensive Care Units (NICUs are particularly susceptible to opportunistic infection. Infected infants have high mortality rates, and survivors often suffer life-long neurological disorders. The causes of many NICU infections go undiagnosed, and there is debate as to the importance of inanimate hospital environments (IHEs in the spread of infections. We used culture-independent next-generation sequencing to survey bacterial diversity in two San Diego NICUs and to track the sources of microbes in these environments. Thirty IHE samples were collected from two Level-Three NICU facilities. We extracted DNA from these samples and amplified the bacterial small subunit (16S ribosomal RNA gene sequence using 'universal' barcoded primers. The purified PCR products were pooled into a single reaction for pyrosequencing, and the data were analyzed using QIIME. On average, we detected 93+/-39 (mean +/- standard deviation bacterial genera per sample in NICU IHEs. Many of the bacterial genera included known opportunistic pathogens, and many were skin-associated (e.g., Propionibacterium. In one NICU, we also detected fecal coliform bacteria (Enterobacteriales in a high proportion of the surface samples. Comparison of these NICU-derived sequences to previously published high-throughput 16S rRNA amplicon studies of other indoor environments (offices, restrooms and healthcare facilities, as well as human- and soil-associated environments, found the majority of the NICU samples to be similar to typical building surface and air samples, with the notable exception of the IHEs which were dominated by Enterobacteriaceae. Our findings provide evidence that NICU IHEs harbor a high diversity of human-associated bacteria and demonstrate the potential utility of molecular methods for identifying and tracking bacterial diversity in NICUs.

  9. A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

    Science.gov (United States)

    Barberán, Albert; Casamayor, Emilio O

    2014-12-01

    There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies. © 2014 John Wiley & Sons Ltd.

  10. Molecular Characterization and Potential of Bacterial Species ...

    African Journals Online (AJOL)

    The 16S rRNA gene of total bacteria community and bacterial isolates were amplified by Polymerase Chain Reaction (PCR) using 16S rRNA primers. Total microbial community DNA amplicons were spliced into the PCR-TRAP Cloning Vector, used to transform competent cells of Escherichia coli and sequenced.

  11. Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle.

    Science.gov (United States)

    Bragina, Anastasia; Berg, Christian; Cardinale, Massimiliano; Shcherbakov, Andrey; Chebotar, Vladimir; Berg, Gabriele

    2012-04-01

    Knowledge about Sphagnum-associated microbial communities, their structure and their origin is important to understand and maintain climate-relevant Sphagnum-dominated bog ecosystems. We studied bacterial communities of two cosmopolitan Sphagnum species, which are well adapted to different abiotic parameters (Sphagnum magellanicum, which are strongly acidic and ombrotrophic, and Sphagnum fallax, which are weakly acidic and mesotrophic), in three Alpine bogs in Austria by a multifaceted approach. Great differences between bacterial fingerprints of both Sphagna were found independently from the site. This remarkable specificity was confirmed by a cloning and a deep sequencing approach. Besides the common Alphaproteobacteria, we found a discriminative spectrum of bacteria; although Gammaproteobacteria dominated S. magellanicum, S. fallax was mainly colonised by Verrucomicrobia and Planctomycetes. Using this information for fluorescent in situ hybridisation analyses, corresponding colonisation patterns for Alphaproteobacteria and Planctomycetes were detected. Bacterial colonies were found in high abundances inside the dead big hyalocytes, but they were always connected with the living chlorocytes. Using multivariate statistical analysis, the abiotic factors nutrient richness and pH were identified to modulate the composition of Sphagnum-specific bacterial communities. Interestingly, we found that the immense bacterial diversity was transferred via the sporophyte to the gametophyte, which can explain the high specificity of Sphagnum-associated bacteria over long distances. In contrast to higher plants, which acquire their bacteria mainly from the environment, mosses as the phylogenetically oldest land plants maintain their bacterial diversity within the whole lifecycle.

  12. Molecular bacterial diversity and bioburden of commercial airliner cabin air

    Energy Technology Data Exchange (ETDEWEB)

    La Duc, M.T.; Stuecker, T.; Venkateswaran, K. [California Inst. of Technology, Pasadena, CA (United States). Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group

    2007-11-15

    Microorganisms that exist in aircraft air systems are considered to be the primary source of microbial contamination that can lead to illness shortly after flying. More than 600 million passengers board commercial airline flights annually in the United States alone. In this study, culture-independent, biomarker-targeted bacterial enumeration and identification strategies were used to estimate total bacterial burden and diversity within the cabin air of commercial airliners. Air-impingement was used to collect samples of microorganisms from 4 flights on 2 commercial carriers. The total viable microbial population ranged from below detection limits to 4.1 x 10{sup 6} cells/m{sup 3} of air. Microbes were found to gradually accumulate from the time of passenger boarding through mid-flight. A sharp decline in bacterial abundance was then observed. Representatives of the {alpha}, {beta} and {gamma} Proteobacteria, as well as Gram-positive bacteria, were isolated in varying abundance. Airline A had large abundances of Neisseria meningitidis rRNA gene sequences and Streptococcus oralis/mitis sequences. Airline B was dominated by pseudomonas synxantha sequences as well as N. meningitidis and S. oralis/mitis. The cabin air samples housed low bacterial diversity and were typically dominated by a particular subset of bacteria, notably opportunistic pathogenic inhabitants of the human respiratory tract and oral cavity. The microbes were found largely around the ventilation ducts and gasper conduits that supply cabin air. 45 refs., 4 tabs., 3 figs.

  13. Bacterial diversity and ecological function in lake water bodies

    OpenAIRE

    Lijuan Ren; Dan He; Peng Xing; Yujing Wang; Qinglong Wu

    2013-01-01

    The healthy development of lake ecosystems is a global issue. Bacteria are not only an integral component of food webs, but also play a key role in controlling and regulating water quality in lake ecosystems. Hence, in order to provide some suggestions for maintaining the long-term and healthy development of lake ecosystems, this review discusses and analyses concepts and assessment of bacterial diversity, the distribution of bacteria communities, mechanisms of formation, and the ecological f...

  14. Bacterial profiling of White Plague Disease in a comparative coral species framework.

    KAUST Repository

    Roder, Cornelia

    2014-01-01

    Coral reefs are threatened throughout the world. A major factor contributing to their decline is outbreaks and propagation of coral diseases. Due to the complexity of coral-associated microbe communities, little is understood in terms of disease agents, hosts and vectors. It is known that compromised health in corals is correlated with shifts in bacterial assemblages colonizing coral mucus and tissue. However, general disease patterns remain, to a large extent, ambiguous as comparative studies over species, regions, or diseases are scarce. Here, we compare bacterial assemblages of samples from healthy (HH) colonies and such displaying signs of White Plague Disease (WPD) of two different coral species (Pavona duerdeni and Porites lutea) from the same reef in Koh Tao, Thailand, using 16S rRNA gene microarrays. In line with other studies, we found an increase of bacterial diversity in diseased (DD) corals, and a higher abundance of taxa from the families that include known coral pathogens (Alteromonadaceae, Rhodobacteraceae, Vibrionaceae). In our comparative framework analysis, we found differences in microbial assemblages between coral species and coral health states. Notably, patterns of bacterial community structures from HH and DD corals were maintained over species boundaries. Moreover, microbes that differentiated the two coral species did not overlap with microbes that were indicative of HH and DD corals. This suggests that while corals harbor distinct species-specific microbial assemblages, disease-specific bacterial abundance patterns exist that are maintained over coral species boundaries.

  15. Characterization of rumen bacterial diversity and fermentation parameters in concentrate fed cattle with and without forage.

    Science.gov (United States)

    Petri, R M; Forster, R J; Yang, W; McKinnon, J J; McAllister, T A

    2012-06-01

    To determine the effects of the removal of forage in high-concentrate diets on rumen fermentation conditions and rumen bacterial populations using culture-independent methods. Detectable bacteria and fermentation parameters were measured in the solid and liquid fractions of digesta from cattle fed two dietary treatments, high concentrate (HC) and high concentrate without forage (HCNF). Comparison of rumen fermentation conditions showed that duration of time spent below pH 5·2 and rumen osmolality were higher in the HCNF treatment. Simpson's index of 16S PCR-DGGE images showed a greater diversity of dominant species in the HCNF treatment. Real-time qPCR showed populations of Fibrobacter succinogenes (P = 0·01) were lower in HCNF than HC diets. Ruminococcus spp., F. succinogenes and Selenomonas ruminantium were at higher (P ≤ 0·05) concentrations in the solid vs the liquid fraction of digesta regardless of diet. The detectable bacterial community structure in the rumen is highly diverse. Reducing diet complexity by removing forage increased bacterial diversity despite the associated reduction in ruminal pH being less conducive for fibrolytic bacterial populations. Quantitative PCR showed that removal of forage from the diet resulted in a decline in the density of some, but not all fibrolytic bacterial species examined. Molecular techniques such as DGGE and qPCR provide an increased understanding of the impacts of dietary changes on the nature of rumen bacterial populations, and conclusions derived using these techniques may not match those previously derived using traditional laboratory culturing techniques. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

  16. Maize Endophytic Bacterial Diversity as Affected by Soil Cultivation History.

    Science.gov (United States)

    Correa-Galeote, David; Bedmar, Eulogio J; Arone, Gregorio J

    2018-01-01

    The bacterial endophytic communities residing within roots of maize ( Zea mays L.) plants cultivated by a sustainable management in soils from the Quechua maize belt (Peruvian Andes) were examined using tags pyrosequencing spanning the V4 and V5 hypervariable regions of the 16S rRNA. Across four replicate libraries, two corresponding to sequences of endophytic bacteria from long time maize-cultivated soils and the other two obtained from fallow soils, 793 bacterial sequences were found that grouped into 188 bacterial operational taxonomic units (OTUs, 97% genetic similarity). The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from fallow soils. A mean of 30 genera were found in the fallow soil libraries and 47 were in those from the maize-cultivated soils. Both alpha and beta diversity indexes showed clear differences between bacterial endophytic populations from plants with different soil cultivation history and that the soils cultivated for long time requires a higher diversity of endophytes. The number of sequences corresponding to main genera Sphingomonas, Herbaspirillum, Bradyrhizobium and Methylophilus in the maize-cultivated libraries were statistically more abundant than those from the fallow soils. Sequences of genera Dyella and Sreptococcus were significantly more abundant in the libraries from the fallow soils. Relative abundance of genera Burkholderia, candidatus Glomeribacter, Staphylococcus, Variovorax, Bacillus and Chitinophaga were similar among libraries. A canonical correspondence analysis of the relative abundance of the main genera showed that the four libraries distributed in two clearly separated groups. Our results suggest that cultivation history is an important driver of endophytic colonization of maize and that after a long time of cultivation of the soil the maize plants need to increase the richness of the bacterial endophytes communities.

  17. Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?

    Directory of Open Access Journals (Sweden)

    Lilibeth N Miranda

    Full Text Available Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1 to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2 determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3 to determine how the microbial community associated with a laboratory strain (P.um.1 established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1 were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads. The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7. The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria were also abundant. Sphingobacteria (Bacteroidetes and Flavobacteria (Bacteroidetes had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes, was abundant. Lewinella (as 66 OTUs was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had

  18. Experimental warming effects on the bacterial community structure and diversity

    Science.gov (United States)

    Kim, W.; Han, S.; Adams, J.; Son, Y.

    2014-12-01

    The objective of this study is to investigate the responses of soil bacterial community to future temperature increase by conducting open-field warming experiment. We conducted an open-field experimental warming system using infra-red heater in 2011 and regulated the temperature of warmed plots by 3oC higher than that of control plots constantly. The seeds of Pinus densiflora, Abies holophylla, Abies koreana, Betula costata, Quercus variabilis, Fraxinus rhynchophylla, and Zelkova serrata were planted in each 1 m × 1 m plot (n=3) in April, 2012. We collected soil samples from the rhizosphere of 7 tree species. DNA was extracted and PCR-amplified for the bacterial 16S gene targeting V1-V3 region. The paired-end sequencing was performed at Beijing Genome Institute (BGI, Hong Kong, China) using 2× 100 bp Hiseq2000 (Illumina). This study aimed to answer the following prediction/hypothesis: 1) Experimental warming will change the structure of soil bacterial community, 2) There will be distinct 'indicator group' which response to warming treatment relatively more sensitive than other groups. 3) Warming treatment will enhance the microbial activity in terms of soil respiration. 4) The rhizoplane bacterial communities for each of 7 tree species will show different response pattern to warming treatment. Since the sequence data does not arrive before the submission deadline, therefore, we would like to present the results and discussions on December 2014, AGU Fall Meeting.

  19. Equilibrium Bird Species Diversity in Atlantic Islands.

    Science.gov (United States)

    Valente, Luis; Illera, Juan Carlos; Havenstein, Katja; Pallien, Tamara; Etienne, Rampal S; Tiedemann, Ralph

    2017-06-05

    Half a century ago, MacArthur and Wilson proposed that the number of species on islands tends toward a dynamic equilibrium diversity around which species richness fluctuates [1]. The current prevailing view in island biogeography accepts the fundamentals of MacArthur and Wilson's theory [2] but questions whether their prediction of equilibrium can be fulfilled over evolutionary timescales, given the unpredictable and ever-changing nature of island geological and biotic features [3-7]. Here we conduct a complete molecular phylogenetic survey of the terrestrial bird species from four oceanic archipelagos that make up the diverse Macaronesian bioregion-the Azores, the Canary Islands, Cape Verde, and Madeira [8, 9]. We estimate the times at which birds colonized and speciated in the four archipelagos, including many previously unsampled endemic and non-endemic taxa and their closest continental relatives. We develop and fit a new multi-archipelago dynamic stochastic model to these data, explicitly incorporating information from 91 taxa, both extant and extinct. Remarkably, we find that all four archipelagos have independently achieved and maintained a dynamic equilibrium over millions of years. Biogeographical rates are homogeneous across archipelagos, except for the Canary Islands, which exhibit higher speciation and colonization. Our finding that the avian communities of the four Macaronesian archipelagos display an equilibrium diversity pattern indicates that a diversity plateau may be rapidly achieved on islands where rates of in situ radiation are low and extinction is high. This study reveals that equilibrium processes may be more prevalent than recently proposed, supporting MacArthur and Wilson's 50-year-old theory. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae

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    Narit Thaochan

    2015-12-01

    Full Text Available The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering and Bactrocera tryoni (Froggatt, was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria which was prominent in all clones. The total bacterial community consisted of Proteobacteria (more than 75% of clones, except in the crop of B. cacuminata where more than 50% of clones belonged to Firmicutes. Firmicutes gave the number of the secondary community structure in the fly’s gut. Four orders, Alpha-, Beta-, Delta- and Gammaproteobacteria and the phyla Firmicutes and Actinobacteria were found in both fruit fly species, while the order Epsilonproteobacteria and the phylum Bacteroidetes were found only in B. tryoni. Two phyla, Actinobacteria and Bacteroidetes, were rare and less frequent in the flies. There was a greater diversity of bacteria in the crop of the two fruit fly species than in the midgut. The midgut of B. tryoni females and the midgut of B. cacuminata males had the lowest bacterial diversity.

  1. Phylogenetically diverse macrophyte community promotes species diversity of mobile epi-benthic invertebrates

    Science.gov (United States)

    Nakamoto, Kenta; Hayakawa, Jun; Kawamura, Tomohiko; Kodama, Masafumi; Yamada, Hideaki; Kitagawa, Takashi; Watanabe, Yoshiro

    2018-07-01

    Various aspects of plant diversity such as species diversity and phylogenetic diversity enhance the species diversity of associated animals in terrestrial systems. In marine systems, however, the effects of macrophyte diversity on the species diversity of associated animals have received little attention. Here, we sampled in a subtropical seagrass-seaweed mixed bed to elucidate the effect of the macrophyte phylogenetic diversity based on the taxonomic relatedness as well as the macrophyte species diversity on species diversity of mobile epi-benthic invertebrates. Using regression analyses for each macrophyte parameter as well as multiple regression analyses, we found that the macrophyte phylogenetic diversity (taxonomic diversity index: Delta) positively influenced the invertebrate species richness and diversity index (H‧). Although the macrophyte species richness and H‧ also positively influenced the invertebrate species richness, the best fit model for invertebrate species richness did not include them, suggesting that the macrophyte species diversity indirectly influenced invertebrate species diversity. Possible explanations of the effects of macrophyte Delta on the invertebrate species diversity were the niche complementarity effect and the selection effect. This is the first study which demonstrates that macrophyte phylogenetic diversity has a strong effect on the species diversity of mobile epi-benthic invertebrates.

  2. Diversity and morphological structure of bacterial communities inhabiting the Diana-Hygieia Thermal Spring (Budapest, Hungary).

    Science.gov (United States)

    Anda, Dóra; Büki, Gabriella; Krett, Gergely; Makk, Judit; Márialigeti, Károly; Erőss, Anita; Mádl-Szőnyi, Judit; Borsodi, Andrea K

    2014-09-01

    The Buda Thermal Karst System is an active hypogenic karst area that offers possibility for the analysis of biogenic cave formation. The aim of the present study was to gain information about morphological structure and genetic diversity of bacterial communities inhabiting the Diana-Hygieia Thermal Spring (DHTS). Using scanning electron microscopy, metal accumulating and unusual reticulated filaments were detected in large numbers in the DHTS biofilm samples. The phyla Actinobacteria, Firmicutes and Proteobacteria were represented by both bacterial strains and molecular clones but phyla Acidobacteria, Chlorobi, Chlorofexi, Gemmatimonadetes, Nitrospirae and Thermotogae only by molecular clones which showed the highest similarity to uncultured clone sequences originating from different environmental sources. The biofilm bacterial community proved to be somewhat more diverse than that of the water sample and the distribution of the dominant bacterial clones was different between biofilm and water samples. The majority of biofilm clones was affiliated with Deltaproteobacteria and Nitrospirae while the largest group of water clones was related to Betaproteobacteria. Considering the metabolic properties of known species related to the strains and molecular clones from DHTS, it can be assumed that these bacterial communities may participate in the local sulphur and iron cycles, and contribute to biogenic cave formation.

  3. Cultivable bacterial diversity along the altitudinal zonation and vegetation range of tropical Eastern Himalaya

    Directory of Open Access Journals (Sweden)

    Nathaniel A. Lyngwi

    2013-03-01

    Full Text Available The Northeastern part of India sprawls over an area of 262 379km² in the Eastern Himalayan range. This constitutes a biodiversity hotspot with high levels of biodiversity and endemism; unfortunately, is also a poorly known area, especially on its microbial diversity. In this study, we assessed cultivable soil bacterial diversity and distribution from lowlands to highlands (34 to 3 990m.a.s.l.. Soil physico-chemical parameters and forest types across the different altitudes were characterized and correlated with bacterial distribution and diversity. Microbes from the soil samples were grown in Nutrient, Muller Hinton and Luria-Bertani agar plates and were initially characterized using biochemical methods. Parameters like dehydrogenase and urease activities, temperature, moisture content, pH, carbon content, bulk density of the sampled soil were measured for each site. Representative isolates were also subjected to 16S rDNA sequence analysis. A total of 155 cultivable bacterial isolates were characterized which were analyzed for richness, evenness and diversity indices. The tropical and sub-tropical forests supported higher bacterial diversity compared to temperate pine, temperate conifer, and sub-alpine rhododendron forests. The 16S rRNA phylogenetic analysis revealed that Firmicutes was the most common group followed by Proteobacteria and Bacteroidetes. Species belonging to the genera Bacillus and Pseudomonas were the most abundant. Bacterial CFU showed positive but insignificant correlation with soil parameters like pH (r=0.208, soil temperature (r=0.303, ambient temperature (r=0.443, soil carbon content (r=0.525, soil bulk density (r=0.268, soil urease (r=0.549 and soil dehydrogenase (r=0.492. Altitude (r=0.561 and soil moisture content (r=-0.051 showed negative correlation. Altitudinal gradient along with the vegetation and soil physico-chemical parameters were found to influence bacterial diversity and distribution. This study points out

  4. Exploiting the aerobic endospore-forming bacterial diversity in saline and hypersaline environments for biosurfactant production.

    Science.gov (United States)

    de Almeida Couto, Camila Rattes; Alvarez, Vanessa Marques; Marques, Joana Montezano; de Azevedo Jurelevicius, Diogo; Seldin, Lucy

    2015-10-28

    Biosurfactants are surface-active biomolecules with great applicability in the food, pharmaceutical and oil industries. Endospore-forming bacteria, which survive for long periods in harsh environments, are described as biosurfactant producers. Although the ubiquity of endospore-forming bacteria in saline and hypersaline environments is well known, studies on the diversity of the endospore-forming and biosurfactant-producing bacterial genera/species in these habitats are underrepresented. In this study, the structure of endospore-forming bacterial communities in sediment/mud samples from Vermelha Lagoon, Massambaba, Dois Rios and Abraão Beaches (saline environments), as well as the Praia Seca salterns (hypersaline environments) was determined via denaturing gradient gel electrophoresis. Bacterial strains were isolated from these environmental samples and further identified using 16S rRNA gene sequencing. Strains presenting emulsification values higher than 30 % were grouped via BOX-PCR, and the culture supernatants of representative strains were subjected to high temperatures and to the presence of up to 20 % NaCl to test their emulsifying activities in these extreme conditions. Mass spectrometry analysis was used to demonstrate the presence of surfactin. A diverse endospore-forming bacterial community was observed in all environments. The 110 bacterial strains isolated from these environmental samples were molecularly identified as belonging to the genera Bacillus, Thalassobacillus, Halobacillus, Paenibacillus, Fictibacillus and Paenisporosarcina. Fifty-two strains showed emulsification values of at least 30%, and they were grouped into 18 BOX groups. The stability of the emulsification values varied when the culture supernatants of representative strains were subjected to high temperatures and to the presence of up to 20% NaCl. The presence of surfactin was demonstrated in one of the most promising strains. The environments studied can harbor endospore

  5. Low Diversity Bacterial Community and the Trapping Activity of Metabolites from Cultivable Bacteria Species in the Female Reproductive System of the Oriental Fruit Fly, Bactrocera dorsalis Hendel (Diptera: Tephritidae

    Directory of Open Access Journals (Sweden)

    Hongyu Zhang

    2012-05-01

    Full Text Available Our goal was to identify the bacteria inhabiting the reproductive system of the female oriental fruit fly, Bactrocera dorsalis (Hendel, and evaluate the chemotaxis of B. dorsalis to the metabolites produced by the bacteria. Based on 16S rRNA-based polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE, 18 operational taxonomic units (OTUs were assigned to the five bacterial classes Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Bacilli and Actinobacteria. Nine OTUs were assigned to Gammaproteobacteria, which was the most highly represented class. Enterobacteriaceae constituted the dominant family, and within this family, three genera and five species were identified, including Enterobacter sakazakii, Klebsiella oxytoca, Klebsiella pneumoniae, Raoultella terrigena and Enterobacter amnigenus. In this set, the first two species were the dominant components, and the latter three species were the minor ones. Finally, we found that the metabolites produced by R. terrigena, K. oxytoca and K. pneumoniae were attractive to the B. dorsalis adults, and in field studies, B. dorsalis adults were most attracted to K. oxytoca. Collectively, our results suggest that the female reproductive system plays an important role in the transfer of enterobacteria from the gut to fruit. Our data may prompt the development of a female-targeted population control strategy for this fly.

  6. Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota

    Science.gov (United States)

    Ellegaard, Kirsten M.; Engel, Philipp

    2016-01-01

    Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities. PMID:27708630

  7. Unexpected variation in neuroanatomy among diverse nematode species

    Directory of Open Access Journals (Sweden)

    Ziduan eHan

    2016-01-01

    Full Text Available Nematodes are considered excellent models for understanding fundamental aspects of neuron function. However, nematodes are less frequently used as models for examining the evolution of nervous systems. While the habitats and behaviors of nematodes are diverse, the neuroanatomy of nematodes is often considered highly conserved. A small number of nematode species greatly influences our understanding of nematode neurobiology. The free-living species Caenorhabditis elegans and, to a lesser extent, the mammalian gastrointestinal parasite Ascaris suum are, historically, the primary sources of knowledge regarding nematode neurobiology. Despite differences in size and habitat, C. elegans and Ascaris suum share a surprisingly similar neuroanatomy. Here, we examined species across several clades in the phylum Nematoda and show that there is a surprising degree of neuroanatomical variation both within and among nematode clades when compared to C. elegans and Ascaris. We found variation in the numbers of neurons in the ventral nerve cord and dye-filling pattern of sensory neurons. For example, we found that Pristionchus pacificus, a bacterial feeding species used for comparative developmental research, had 20% fewer ventral cord neurons compared to C. elegans. Steinernema carpocapse, an insect-parasitic nematode capable of jumping behavior, had 40% more ventral cord neurons than C. elegans. Interestingly, the non-jumping congeneric nematode, S. glaseri showed an identical number of ventral cord neurons as S. carpocapsae. There was also variability in the timing of neurodevelopment of the ventral cord with two of five species that hatch as second-stage juveniles showing delayed neurodevelopment. We also found unexpected variation in the dye-filling of sensory neurons among examined species. Again, sensory neuron dye-filling pattern did not strictly correlate with phylogeny. Our results demonstrate that variation in nematode neuroanatomy is more prevalent

  8. Changes in Soil Bacterial Communities and Diversity in ...

    Science.gov (United States)

    Silver-induced selective pressure is becoming increasingly important due to the growing use of silver (Ag) as an antimicrobial agent in biomedical and commercial products. With demonstrated links between environmental resistomes and clinical pathogens, it is important to identify microbial profiles related to silver tolerance/resistance. We investigated the effects of ionic Ag stress on soil bacterial communities and identified resistant/persistant bacterial populations. Silver treatments of 50 - 400 mg Ag kg-1 soil were established in five soils. Chemical lability measurements using diffusive gradients in thin-film devices confirmed that significant (albeit decreasing) labile Ag concentrations were present throughout the 9-month incubation period. Synchrotron X-ray absorption near edge structure spectroscopy demonstrate that this decreasing lability was due to changes in Ag speciation to less soluble forms such as Ag0 and Ag2S. Real-time PCR and Illumina MiSeq screening of 16S rRNA bacterial genes showed β-diversity in response to Ag pressure, and immediate and significant reductions in 16S rRNA gene counts with varying degrees of recovery. These effects were more strongly influenced by exposure time than by Ag dose at these rates. Ag-selected dominant OTUs principally resided in known persister taxa (mainly Gram positive), including metal-tolerant bacteria and slow-growing Mycobacteria. Soil microbial communities have been implicated as sources of an

  9. Molecular analysis of the bacterial diversity in uranium mill tailings

    International Nuclear Information System (INIS)

    Geissler, A.

    2003-04-01

    A culture-independent molecular approach has been applied to investigate the bacterial diversity in three uranium contaminated sites. The three analysed soil samples have been collected from the uranium waste pile Haberland near Johanngeorgenstadt (Germany), from the uranium mill tailings in Gunnison, Colorado (USA) and from the uranium mill tailings in Shiprock, New Mexico (USA). The 16S rDNA fragments which has been isolated through direct lysis of the whole-DNA were amplified by the use of the universal primers 16S 43f and 16S 1404r and cloned. With restriction fragment length polymorphismus (RFLP) were the clones screened and one representative of all RFLP types that occurred more than once in the clone library was sequenced and analysed. In spite of the contamination a considerable diversity and significant differences in the composition of the natural bacterial communities in these three sites have been found. In the sample collected from the waste pile Haberland near Johanngeorgenstadt α-Proteobacteria and representatives of the Holophaga/Acidobacterium were numerically predominant. The distribution of bacteria in the sample collected from uranium mill tailings Gunnison was very similar to those found in the Haberland waste pile, but there were found besides α-Proteobacteria and representatives of Holophaga/Acidobacterium a lot of γ-Proteobacteria. The structure of the bacterial community in the sample collected from the uranium mill tailings Shiprock was significantly different. Only some representatives of the Holophaga/Acidobacterium and α-Proteobacteria were represented. Large populations of Bacilli, γ-Proteobacteria and green non sulfur bacteria were dominant in this sample. (orig.)

  10. Bacterial Diversity Associated with the Coccolithophorid Algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii

    Directory of Open Access Journals (Sweden)

    David H. Green

    2015-01-01

    Full Text Available Coccolithophores are unicellular calcifying marine phytoplankton that can form large and conspicuous blooms in the oceans and make significant contributions to oceanic carbon cycling and atmospheric CO2 regulation. Despite their importance, the bacterial diversity associated with these algae has not been explored for ecological or biotechnological reasons. Bacterial membership of Emiliania huxleyi and Coccolithus pelagicus f. braarudii cultures was assessed using cultivation and cultivation-independent methods. The communities were species rich compared to other phytoplankton cultures. Community analysis identified specific taxa which cooccur in all cultures (Marinobacter and Marivita. Hydrocarbon-degrading bacteria were found in all cultures. The presence of Acidobacteria, Acidimicrobidae, Schlegelella, and Thermomonas was unprecedented but were potentially explained by calcification associated with coccolith production. One strain of Acidobacteria was cultivated and is closely related to a marine Acidobacteria isolated from a sponge. From this assessment of the bacterial diversity of coccolithophores, a number of biotechnological opportunities are evident, from bioprospecting for novel taxa such as Acidobacteria to helping understand the relationship between obligate hydrocarbonoclastic bacteria occurrence with phytoplankton and to revealing bacterial taxa that have a specific association with algae and may be suitable candidates as a means to improve the efficiency of mass algal cultivation.

  11. Archaeal and bacterial diversity in two hot spring microbial mats from a geothermal region in Romania.

    Science.gov (United States)

    Coman, Cristian; Drugă, Bogdan; Hegedus, Adriana; Sicora, Cosmin; Dragoş, Nicolae

    2013-05-01

    The diversity of archaea and bacteria was investigated in two slightly alkaline, mesophilic hot springs from the Western Plain of Romania. Phylogenetic analysis showed a low diversity of Archaea, only three Euryarchaeota taxa being detected: Methanomethylovorans thermophila, Methanomassiliicoccus luminyensis and Methanococcus aeolicus. Twelve major bacterial groups were identified, both springs being dominated by Cyanobacteria, Chloroflexi and Proteobacteria. While at the phylum/class-level the microbial mats share a similar biodiversity; at the species level the geothermal springs investigated seem to be colonized by specific consortia. The dominant taxa were filamentous heterocyst-containing Fischerella, at 45 °C and non-heterocyst Leptolyngbya and Geitlerinema, at 55 °C. Other bacterial taxa (Thauera sp., Methyloversatilis universalis, Pannonibacter phragmitetus, Polymorphum gilvum, Metallibacterium sp. and Spartobacteria) were observed for the first time in association with a geothermal habitat. Based on their bacterial diversity the two mats were clustered together with other similar habitats from Europe and part of Asia, most likely the water temperature playing a major role in the formation of specific microbial communities that colonize the investigated thermal springs.

  12. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

    Science.gov (United States)

    Maslov, Sergei; Sneppen, Kim

    2017-01-01

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity. PMID:28051127

  13. Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest.

    Directory of Open Access Journals (Sweden)

    Zhenping Yang

    Full Text Available As the major crops in north China, spring crops are usually planted from April through May every spring and harvested in fall. Wheat is also a very common crop traditionally planted in fall or spring and harvested in summer year by year. This continuous cropping system exhibited the disadvantages of reducing the fertility of soil through decreasing microbial diversity. Thus, management of microbial diversity in the rhizosphere plays a vital role in sustainable crop production. In this study, ten common spring crops in north China were chosen sole-cropped and four were chosen intercropped with peanut in wheat fields after harvest. Denaturing gradient gel electrophoresis (DGGE and DNA sequencing of one 16S rDNA fragment were used to analyze the bacterial diversity and species identification. DGGE profiles showed the bacterial community diversity in rhizosphere soil samples varied among various crops under different cropping systems, more diverse under intercropping system than under sole-cropping. Some intercropping-specific bands in DGGE profiles suggested that several bacterial species were stimulated by intercropping systems specifically. Furthermore, the identification of these dominant and functional bacteria by DNA sequencing indicated that intercropping systems are more beneficial to improve soil fertility. Compared to intercropping systems, we also observed changes in microbial community of rhizosphere soil under sole-crops. The rhizosphere bacterial community structure in spring crops showed a strong crop species-specific pattern. More importantly, Empedobacter brevis, a typical plant pathogen, was only found in the carrot rhizosphere, suggesting carrot should be sown prudently. In conclusion, our study demonstrated that crop species and cropping systems had significant effects on bacterial community diversity in the rhizosphere soils. We strongly suggest sorghum, glutinous millet and buckwheat could be taken into account as intercropping

  14. Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest.

    Science.gov (United States)

    Yang, Zhenping; Yang, Wenping; Li, Shengcai; Hao, Jiaomin; Su, Zhifeng; Sun, Min; Gao, Zhiqiang; Zhang, Chunlai

    2016-01-01

    As the major crops in north China, spring crops are usually planted from April through May every spring and harvested in fall. Wheat is also a very common crop traditionally planted in fall or spring and harvested in summer year by year. This continuous cropping system exhibited the disadvantages of reducing the fertility of soil through decreasing microbial diversity. Thus, management of microbial diversity in the rhizosphere plays a vital role in sustainable crop production. In this study, ten common spring crops in north China were chosen sole-cropped and four were chosen intercropped with peanut in wheat fields after harvest. Denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of one 16S rDNA fragment were used to analyze the bacterial diversity and species identification. DGGE profiles showed the bacterial community diversity in rhizosphere soil samples varied among various crops under different cropping systems, more diverse under intercropping system than under sole-cropping. Some intercropping-specific bands in DGGE profiles suggested that several bacterial species were stimulated by intercropping systems specifically. Furthermore, the identification of these dominant and functional bacteria by DNA sequencing indicated that intercropping systems are more beneficial to improve soil fertility. Compared to intercropping systems, we also observed changes in microbial community of rhizosphere soil under sole-crops. The rhizosphere bacterial community structure in spring crops showed a strong crop species-specific pattern. More importantly, Empedobacter brevis, a typical plant pathogen, was only found in the carrot rhizosphere, suggesting carrot should be sown prudently. In conclusion, our study demonstrated that crop species and cropping systems had significant effects on bacterial community diversity in the rhizosphere soils. We strongly suggest sorghum, glutinous millet and buckwheat could be taken into account as intercropping crops with peanut

  15. High bacterial diversity in epilithic biofilms of oligotrophic mountain lakes.

    Science.gov (United States)

    Bartrons, Mireia; Catalan, Jordi; Casamayor, Emilio O

    2012-11-01

    Benthic microbial biofilms attached to rocks (epilithic) are major sites of carbon cycling and can dominate ecosystem primary production in oligotrophic lakes. We studied the bacterial community composition of littoral epilithic biofilms in five connected oligotrophic high mountain lakes located at different altitudes by genetic fingerprinting and clone libraries of the 16S rRNA gene. Different intra-lake samples were analyzed, and consistent changes in community structure (chlorophyll a and organic matter contents, and bacterial community composition) were observed along the altitudinal gradient, particularly related with the location of the lake above or below the treeline. Epilithic biofilm genetic fingerprints were both more diverse among lakes than within lakes and significantly different between montane (below the tree line) and alpine lakes (above the tree line). The genetic richness in the epilithic biofilm was much higher than in the plankton of the same lacustrine area studied in previous works, with significantly idiosyncratic phylogenetic composition (specifically distinct from lake plankton or mountain soils). Data suggest the coexistence of aerobic, anaerobic, phototrophic, and chemotrophic microorganisms in the biofilm, Bacteroidetes and Cyanobacteria being the most important bacterial taxa, followed by Alpha-, Beta-, Gamma-, and Deltaproteobacteria, Chlorobi, Planctomycetes, and Verrucomicrobia. The degree of novelty was especially high for epilithic Bacteroidetes, and up to 50 % of the sequences formed monophyletic clusters distantly related to any previously reported sequence. More than 35 % of the total sequences matched at <95 % identity to any previously reported 16S rRNA gene, indicating that alpine epilithic biofilms are unexplored habitats that contain a substantial degree of novelty within a short geographical distance. Further research is needed to determine whether these communities are involved in more biogeochemical pathways than

  16. Distinct soil bacterial communities revealed under a diversely managed agroecosystem.

    Directory of Open Access Journals (Sweden)

    Raymon S Shange

    Full Text Available Land-use change and management practices are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, their effect on the soil microbial community and their subsequent influence on soil function is still difficult to quantify. Recent applications of molecular techniques to soil biology, especially the use of 16S rRNA, are helping to bridge this gap. In this study, the influence of three land-use systems within a demonstration farm were evaluated with a view to further understand how these practices may impact observed soil bacterial communities. Replicate soil samples collected from the three land-use systems (grazed pine forest, cultivated crop, and grazed pasture on a single soil type. High throughput 16S rRNA gene pyrosequencing was used to generate sequence datasets. The different land use systems showed distinction in the structure of their bacterial communities with respect to the differences detected in cluster analysis as well as diversity indices. Specific taxa, particularly Actinobacteria, Acidobacteria, and classes of Proteobacteria, showed significant shifts across the land-use strata. Families belonging to these taxa broke with notions of copio- and oligotrphy at the class level, as many of the less abundant groups of families of Actinobacteria showed a propensity for soil environments with reduced carbon/nutrient availability. Orders Actinomycetales and Solirubrobacterales showed their highest abundance in the heavily disturbed cultivated system despite the lowest soil organic carbon (SOC values across the site. Selected soil properties ([SOC], total nitrogen [TN], soil texture, phosphodiesterase [PD], alkaline phosphatase [APA], acid phosphatase [ACP] activity, and pH also differed significantly across land-use regimes, with SOM, PD, and pH showing variation consistent with shifts in community structure and composition. These results suggest that use of

  17. Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia

    KAUST Repository

    Arnaud-Haond, S.; Aires, T.; Candeias, R.; Teixeira, S. J. L; Duarte, Carlos M.; Valero, M.; Serrã o, E. A.

    2017-01-01

    Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and ß diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in Southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions. This article is protected by copyright. All rights reserved.

  18. Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia

    KAUST Repository

    Arnaud-Haond, S.

    2017-01-30

    Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and ß diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in Southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions. This article is protected by copyright. All rights reserved.

  19. Genetic diversity within a dominant plant outweighs plant species diversity in structuring an arthropod community.

    Science.gov (United States)

    Crawford, Kerri M; Rudgers, Jennifer A

    2013-05-01

    Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We (1) independently manipulated plant species diversity, (2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and (3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive nonadditive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species

  20. Species richness and trophic diversity increase decomposition in a co-evolved food web.

    Directory of Open Access Journals (Sweden)

    Benjamin Baiser

    Full Text Available Ecological communities show great variation in species richness, composition and food web structure across similar and diverse ecosystems. Knowledge of how this biodiversity relates to ecosystem functioning is important for understanding the maintenance of diversity and the potential effects of species losses and gains on ecosystems. While research often focuses on how variation in species richness influences ecosystem processes, assessing species richness in a food web context can provide further insight into the relationship between diversity and ecosystem functioning and elucidate potential mechanisms underpinning this relationship. Here, we assessed how species richness and trophic diversity affect decomposition rates in a complete aquatic food web: the five trophic level web that occurs within water-filled leaves of the northern pitcher plant, Sarracenia purpurea. We identified a trophic cascade in which top-predators--larvae of the pitcher-plant mosquito--indirectly increased bacterial decomposition by preying on bactivorous protozoa. Our data also revealed a facultative relationship in which larvae of the pitcher-plant midge increased bacterial decomposition by shredding detritus. These important interactions occur only in food webs with high trophic diversity, which in turn only occur in food webs with high species richness. We show that species richness and trophic diversity underlie strong linkages between food web structure and dynamics that influence ecosystem functioning. The importance of trophic diversity and species interactions in determining how biodiversity relates to ecosystem functioning suggests that simply focusing on species richness does not give a complete picture as to how ecosystems may change with the loss or gain of species.

  1. Species diversity: Benthonic Foraminifera in Western North Atlantic

    Science.gov (United States)

    Buzas, M.A.; Gibson, T.G.

    1969-01-01

    Maximum species diversity occurs at abyssal depths of greater than 2500 meters. Other diversity peaks occur at depths of 35 to 45 meters and 100 to 200 meters. The peak at 35 to 45 meters is due to species equitability, whereas the other two peaks correspond to an increase in the number of species.

  2. Genetic diversity and species diversity of stream fishes covary across a land-use gradient

    Science.gov (United States)

    Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

    2012-01-01

    Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

  3. Plants of the fynbos biome harbour host species-specific bacterial communities.

    Science.gov (United States)

    Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

    2016-08-01

    The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Pyrosequencing based assessment of bacterial diversity in Turkish Rhipicephalus annulatus and Dermacentor marginatus ticks (Acari: Ixodidae).

    Science.gov (United States)

    Tekin, Saban; Dowd, Scot E; Davinic, Marko; Bursali, Ahmet; Keskin, Adem

    2017-03-01

    Ticks continue to be a threat to human and animal health in Turkey, as they are considered important vectors of human and animal diseases. The objectives of this investigation are to characterize the microbial communities of two tick species, Rhipicephalus annulatus and Dermacenter marginatus, analyze patterns of co-occurrence among microbial taxa, identify and compare pathogens contributing human diseases, and determine whether avirulent symbionts could exclude human pathogens from tick communities. Furthermore, this study explores a microbiome of the R. annulatus and D. marginatus via the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) technique to describe their bacterial diversity. Pyrosequencing was performed on adult males and females isolated from humans from two high-risk Turkish provinces, Sivas and Amasya, during tick outbreaks in 2009. A total of 36,253 sequences were utilized for analyses of the 8 tick samples. Several pathogenic genera such as Francisella, Coxiella, Rickettsia, and Shigella were detected in the ticks tested. The most distinguishable difference between the two species of ticks was the lack of known human pathogen Rickettsia in R. annulatus and in samples 9 and 10 of D. marginatus. These samples had higher relative abundance of Flavobacterium sp., Curvibacter sp., Acidovorax sp., and Bacteroidaceae genera mostly representing symbionts which form a large component of normal tick microbiota. The outcome of this study is consistent with the predictions of the community ecological theory that diversity-rich bacteriomes are more resistant to bacterial invasion (and consequent pathogen dissemination) than diversity-deprived ones.

  5. Revegetation of the riparian zone of the Three Gorges Dam Reservoir leads to increased soil bacterial diversity.

    Science.gov (United States)

    Ren, Qingshui; Li, Changxiao; Yang, Wenhang; Song, Hong; Ma, Peng; Wang, Chaoying; Schneider, Rebecca L; Morreale, Stephen J

    2018-06-06

    As one of the most active components in soil, bacteria can affect soil physicochemical properties, its biological characteristics, and even its quality and health. We characterized dynamics of the soil bacterial diversity in planted (with Taxodium distichum) and unplanted soil in the riparian zone of the Three Gorges Dam Reservoir (TGDR), in southwestern China, in order to accurately quantify the changes in long-term soil bacterial community structure after revegetation. Measurements were taken annually in situ in the TGDR over the course of 5 years, from 2012 to 2016. Soil chemical properties and bacterial diversity were analyzed in both the planted and unplanted soil. After revegetation, the soil chemical properties in planted soil were significantly different than in unplanted soil. The effects of treatment, time, and the interaction of both time and treatment had significant impacts on most diversity indices. Specifically, the bacterial community diversity indices in planted soil were significantly higher and more stable than that in unplanted soil. The correlation analyses indicated that the diversity indices correlated with the pH value, organic matter, and soil available nutrients. After revegetation in the riparian zone of the TGDR, the soil quality and health is closely related to the observed bacterial diversity, and a higher bacterial diversity avails the maintenance of soil functionality. Thus, more reforestation should be carried out in the riparian zone of the TGDR, so as to effectively mitigate the negative ecological impacts of the dam. Vegetating the reservoir banks with Taxodium distichum proved successful, but planting mixed stands of native tree species could promote even higher riparian soil biodiversity and improved levels of ecosystem functioning within the TGDR.

  6. Dissolution and degradation of crude oil droplets by different bacterial species and consortia by microcosm microfluidics

    Science.gov (United States)

    Jalali, Maryam; Sheng, Jian

    2017-11-01

    Bacteria are involved in cleanup and degradation of crude oil in polluted marine and soil environments. A number of bacterial species have been identified for consuming petroleum hydrocarbons with diverse metabolic capabilities. We conducted laboratory experiments to investigate bacterial consumption by monitoring the volume change to oil droplets as well as effects of oil droplet size on this process. To conduct our study, we developed a micro-bioassay containing an enclosed chamber with bottom substrate printed with stationary oil microdroplets and a digital holographic interferometer (DHI). The morphology of microdroplets was monitored in real time over 100 hours and instantaneous flow field was also measured by digital holographic microscope. The substrates with printed oil droplets were further evaluated with atomic force microscopy (AFM) at the end of each experiment. Three different bacteria species, Pseudomonas sp, Alcanivorax borkumensis, and Marinobacter hydrocarbonoclasticus, as well as six bacterial consortia were used in this study. The results show that droplets smaller than 20µm in diameter are not subject to bacterial degradation and the volume of droplet did not change beyond dissolution. Substantial species-specific behaviors have been observed in isolates. The experiments of consortia and various flow shears on biodegradation and dissolution are ongoing and will be reported.

  7. Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems.

    Science.gov (United States)

    Rampelotto, Pabulo Henrique; de Siqueira Ferreira, Adão; Barboza, Anthony Diego Muller; Roesch, Luiz Fernando Wurdig

    2013-10-01

    The Brazilian Savanna, also known as "Cerrado", is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.

  8. Methanol removal efficiency and bacterial diversity of an activated carbon biofilter.

    Science.gov (United States)

    Babbitt, Callie W; Pacheco, Adriana; Lindner, Angela S

    2009-12-01

    Motivated by the need to establish an economical and environmentally friendly methanol control technology for the pulp and paper industry, a bench-scale activated carbon biofiltration system was developed. This system was evaluated for its performance in removing methanol from an artificially contaminated air stream and characterized for its bacterial diversity over time, under varied methanol loading rates, and in different spatial regions of the filter. The biofilter system, composed of a novel packing mixture, provided an excellent support for growth and activity of methanol-degrading bacteria, resulting in approximately 100% methanol removal efficiency for loading rates of 1-17 g/m(3) packing/h, when operated both with and without inoculum containing enriched methanol-degrading bacteria. Although bacterial diversity and abundance varied over the length of the biofilter, the populations present rapidly formed a stable community that was maintained over the entire 138-day operation of the system and through variable operating conditions, as observed by PCR-DGGE methods that targeted all bacteria as well as specific methanol-oxidizing microorganisms. Phylogenetic analysis of bands excised and sequenced from DGGE gels indicated that the biofilter system supported a diverse community of methanol-degrading bacteria, with high similarity to species in the genera Methylophilus (beta-proteobacteria), Hyphomicrobium and Methylocella (both alpha-proteobacteria).

  9. Autotrophic and heterotrophic bacterial diversity from Yucca Mountain

    International Nuclear Information System (INIS)

    Khalil, M.; Haldeman, D.L.; Igbinovia, A.; Castro, P.

    1996-01-01

    A basic understanding of the types and functions of microbiota present within the deep subsurface of Yucca Mountain will be important in terms of modeling the long term stability of a nuclear waste repository. Microorganisms can degrade building materials used in tunnel construction such as concrete and steel. For example, high concentrations of nitrifying bacteria, may cause corrosion of concrete due to the release of nitric acid. Likewise, sulfur-oxidizing and iron-oxidizing bacteria have been implicated in microbially influenced corrosion (MIC), and may contribute to the degradation of waste packages. In addition, the metabolic activities of microbiota may alter the geochemistry of surrounding environments, which may in turn influence the permeability of subsurface strata and the fate of radioactive compounds. Microorganisms that play roles in these processes have diverse methods of obtaining the energy required for growth and metabolism and have been recovered from a wide range of environments, including the deep subsurface. The purpose of this research was to determine if these bacterial groups, important to the long-term success of a high-level nuclear waste repository, were indigenous to Yucca Mountain

  10. Identification and characterization of bacterial symbionts in three species of filth fly parasitoids.

    Science.gov (United States)

    Betelman, Kfir; Caspi-Fluger, Ayelet; Shamir, Maayan; Chiel, Elad

    2017-09-01

    Facultative bacterial symbionts are widespread among insects and have diverse effects on their biology. Here, we focused on bacterial symbionts of three ecologically and economically important filth flies parasitoid species-Spalangia cameroni, Spalangia endius and Muscidifurax raptor. Both Spalangia species harbored a Sodalis bacterium that is closely related to Spalangia praecaptivus (a free-living bacterium) and to Sodalis symbionts of weevils. This is the only case of Sodalis infection in the important order Hymenoptera. We also found, for the first time in this parasitoid guild, a Rickettsia infecting the two Spalangia spp., albeit in much higher prevalence in S. cameroni. Molecular and phylogenetic analyses revealed that it is closely related to Rickettsia felis and other Rickettsia species from the 'transitional' group. All three parasitoid species harbored Wolbachia. Using multi-locus sequence typing, we found that M. raptor harbors a single Wolbachia strain whereas the Spalangia spp. have multiple strains. By controlled crossings, we found that Wolbachia infection in S. endius causes incomplete cytoplasmic incompatibility and increased longevity, thereby promoting Wolbachia's spread. In contrast, no effects of Wolbachia on the reproduction and longevity of M. raptor were found. This study underscores the diversity and nature of symbiotic interactions between microbes and insects. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Genetic calibration of species diversity among North America's freshwater fishes.

    Science.gov (United States)

    April, Julien; Mayden, Richard L; Hanner, Robert H; Bernatchez, Louis

    2011-06-28

    Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required.

  12. Nutritional diversity of leafy amaranth species grown in Kenya ...

    African Journals Online (AJOL)

    Objectives: Despite the availability of many species of amaranth in Kenya, there is inadequate information on their nutritional diversity and how they can be best used in mitigation of malnutrition. Hence, this study was aimed at investigating the nutritional diversity of five leafy amaranth species grown in Kenya. Methodology ...

  13. Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity.

    Science.gov (United States)

    Pardikes, Nicholas A; Lumpkin, Will; Hurtado, Paul J; Dyer, Lee A

    2018-01-01

    Most of earth's biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships

  14. Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage

    Directory of Open Access Journals (Sweden)

    Victoria Mesa

    2017-09-01

    Full Text Available Acid mine drainages are characterized by their low pH and the presence of dissolved toxic metallic species. Microorganisms survive in different microhabitats within the ecosystem, namely water, sediments, and biofilms. In this report, we surveyed the microbial diversity within all domains of life in the different microhabitats at Los Rueldos abandoned mercury underground mine (NW Spain, and predicted bacterial function based on community composition. Sediment samples contained higher proportions of soil bacteria (AD3, Acidobacteria, as well as Crenarchaeota and Methanomassiliicoccaceae archaea. Oxic and hypoxic biofilm samples were enriched in bacterial iron oxidizers from the genus Leptospirillum, order Acidithiobacillales, class Betaproteobacteria, and archaea from the class Thermoplasmata. Water samples were enriched in Cyanobacteria and Thermoplasmata archaea at a 3–98% of the sunlight influence, whilst Betaproteobacteria, Thermoplasmata archaea, and Micrarchaea dominated in acid water collected in total darkness. Stalactites hanging from the Fe-rich mine ceiling were dominated by the neutrophilic iron oxidizer Gallionella and other lineages that were absent in the rest of the microhabitats (e.g., Chlorobi, Chloroflexi. Eukaryotes were detected in biofilms and open-air water samples, and belonged mainly to clades SAR (Alveolata and Stramenopiles, and Opisthokonta (Fungi. Oxic and hypoxic biofilms displayed higher proportions of ciliates (Gonostomum, Oxytricha, whereas water samples were enriched in fungi (Paramicrosporidium and unknown microbial Helotiales. Predicted function through bacterial community composition suggested adaptive evolutive convergence of function in heterogeneous communities. Our study showcases a broad description of the microbial diversity across different microhabitats in the same environment and expands the knowledge on the diversity of microbial eukaryotes in AMD habitats.

  15. Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage

    Science.gov (United States)

    Mesa, Victoria; Gallego, Jose L. R.; González-Gil, Ricardo; Lauga, Béatrice; Sánchez, Jesús; Méndez-García, Celia; Peláez, Ana I.

    2017-01-01

    Acid mine drainages are characterized by their low pH and the presence of dissolved toxic metallic species. Microorganisms survive in different microhabitats within the ecosystem, namely water, sediments, and biofilms. In this report, we surveyed the microbial diversity within all domains of life in the different microhabitats at Los Rueldos abandoned mercury underground mine (NW Spain), and predicted bacterial function based on community composition. Sediment samples contained higher proportions of soil bacteria (AD3, Acidobacteria), as well as Crenarchaeota and Methanomassiliicoccaceae archaea. Oxic and hypoxic biofilm samples were enriched in bacterial iron oxidizers from the genus Leptospirillum, order Acidithiobacillales, class Betaproteobacteria, and archaea from the class Thermoplasmata. Water samples were enriched in Cyanobacteria and Thermoplasmata archaea at a 3–98% of the sunlight influence, whilst Betaproteobacteria, Thermoplasmata archaea, and Micrarchaea dominated in acid water collected in total darkness. Stalactites hanging from the Fe-rich mine ceiling were dominated by the neutrophilic iron oxidizer Gallionella and other lineages that were absent in the rest of the microhabitats (e.g., Chlorobi, Chloroflexi). Eukaryotes were detected in biofilms and open-air water samples, and belonged mainly to clades SAR (Alveolata and Stramenopiles), and Opisthokonta (Fungi). Oxic and hypoxic biofilms displayed higher proportions of ciliates (Gonostomum, Oxytricha), whereas water samples were enriched in fungi (Paramicrosporidium and unknown microbial Helotiales). Predicted function through bacterial community composition suggested adaptive evolutive convergence of function in heterogeneous communities. Our study showcases a broad description of the microbial diversity across different microhabitats in the same environment and expands the knowledge on the diversity of microbial eukaryotes in AMD habitats. PMID:28955322

  16. Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis.

    Directory of Open Access Journals (Sweden)

    Robert J Gruninger

    Full Text Available The North American Beaver (Castor canadensis is the second largest living rodent and an iconic symbol of Canada. The beaver is a semi-aquatic browser whose diet consists of lignocellulose from a variety of plants. The beaver is a hindgut fermenter and has an enlarged ceacum that houses a complex microbiome. There have been few studies examining the microbial diversity in gastrointestinal tract of hindgut fermenting herbivores. To examine the bacterial and archaeal communities inhabiting the gastrointestinal tract of the beaver, the microbiome of the ceacum and feaces was examined using culture-independent methods. DNA from the microbial community of the ceacum and feaces of 4 adult beavers was extracted, and the16S rRNA gene was sequenced using either bacterial or archaeal specific primers. A total of 1447 and 1435 unique bacterial OTUs were sequenced from the ceacum and feaces, respectively. On average, the majority of OTUs within the ceacum were classified as Bacteroidetes (49.2% and Firmicutes (47.6%. The feaces was also dominated by OTUs from Bacteroidetes (36.8% and Firmicutes (58.9%. The composition of bacterial community was not significantly different among animals. The composition of the ceacal and feacal microbiome differed, but this difference is due to changes in the abundance of closely related OTUs, not because of major differences in the taxonomic composition of the communities. Within these communities, known degraders of lignocellulose were identified. In contrast, to the bacterial microbiome, the archaeal community was dominated by a single species of methanogen, Methanosphaera stadtmanae. The data presented here provide the first insight into the microbial community within the hindgut of the beaver.

  17. Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis).

    Science.gov (United States)

    Gruninger, Robert J; McAllister, Tim A; Forster, Robert J

    2016-01-01

    The North American Beaver (Castor canadensis) is the second largest living rodent and an iconic symbol of Canada. The beaver is a semi-aquatic browser whose diet consists of lignocellulose from a variety of plants. The beaver is a hindgut fermenter and has an enlarged ceacum that houses a complex microbiome. There have been few studies examining the microbial diversity in gastrointestinal tract of hindgut fermenting herbivores. To examine the bacterial and archaeal communities inhabiting the gastrointestinal tract of the beaver, the microbiome of the ceacum and feaces was examined using culture-independent methods. DNA from the microbial community of the ceacum and feaces of 4 adult beavers was extracted, and the16S rRNA gene was sequenced using either bacterial or archaeal specific primers. A total of 1447 and 1435 unique bacterial OTUs were sequenced from the ceacum and feaces, respectively. On average, the majority of OTUs within the ceacum were classified as Bacteroidetes (49.2%) and Firmicutes (47.6%). The feaces was also dominated by OTUs from Bacteroidetes (36.8%) and Firmicutes (58.9%). The composition of bacterial community was not significantly different among animals. The composition of the ceacal and feacal microbiome differed, but this difference is due to changes in the abundance of closely related OTUs, not because of major differences in the taxonomic composition of the communities. Within these communities, known degraders of lignocellulose were identified. In contrast, to the bacterial microbiome, the archaeal community was dominated by a single species of methanogen, Methanosphaera stadtmanae. The data presented here provide the first insight into the microbial community within the hindgut of the beaver.

  18. Microbiological quality and bacterial diversity of the tropical oyster Crassostrea rhizophorae in a monitored farming system and from natural stocks.

    Science.gov (United States)

    Silva Neta, M T; Maciel, B M; Lopes, A T S; Marques, E L S; Rezende, R P; Boehs, G

    2015-12-02

    Microbiological evaluation is one of the most important parameters for analyzing the viability of an oyster farming system, which addresses public health and ecological concerns. Here, the microbiological quality of the oyster Crassostrea rhizophorae cultivated in a monitored environment and from natural beds in Bahia, northeastern Brazil, was determined. Bacterial diversity in oysters was measured by polymerase chain reaction-denaturing gradient gel electrophoresis. Sequence analysis revealed that most bacterial species showed similarity with uncultured or unidentified bacteria from environmental samples, and were clustered into the phylum Proteobacteria. Diverse bacteria from cultivated (monitored) oyster samples were grouped in the same cluster with a high similarity index (above 79%). Microbiological analyses revealed that these oysters did not contain pathogens. These results reflect the natural balance of the microbial communities essential to the maintenance of health and in inhibiting pathogen colonization in the oyster. On the other hand, bacterial diversity of samples from native stocks in extractive areas displayed a similarity index varying between 55 and 77%, and all samples were clustered separately from each other and from the cluster of samples derived from the cultivation area. Microbiological analyses showed that oysters from the extractive area were not fit for human consumption. This reflected a different composition of the microbial community in this area, probably resulting from anthropic impact. Our study also demonstrated that low temperatures and high rainfall limits the bacterial concentration in tropical oysters. This is the first study analyzing the total bacterial community profiles of the oyster C. rhizophorae.

  19. Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species

    Directory of Open Access Journals (Sweden)

    Lena Waidele

    2017-12-01

    Full Text Available The gut microbiome of lower termites comprises protists and bacteria that help these insects to digest cellulose and to thrive on wood. The composition of the termite gut microbiome correlates with phylogenetic distance of the animal host and host ecology (diet in termites collected from their natural environment. However, carryover of transient microbes from host collection sites are an experimental concern and might contribute to the ecological imprints on the termite gut microbiome. Here, we set out to test whether an ecological imprint on the termite gut microbiome remains, when focusing on the persistent microbiome. Therefore, we kept five termite species under strictly controlled dietary conditions and subsequently profiled their protist and bacterial gut microbial communities using 18S and 16S rRNA gene amplicon sequencing. The species differed in their ecology; while three of the investigated species were wood-dwellers that feed on the piece of wood they live in and never leave except for the mating flight, the other two species were foragers that regularly leave their nests to forage for food. Despite these prominent ecological differences, protist microbiome structure aligned with phylogenetic relatedness of termite host species. Conversely, bacterial communities seemed more flexible, suggesting that microbiome structure aligned more strongly with the foraging and wood-dwelling ecologies. Interestingly, protist and bacterial community alpha-diversity correlated, suggesting either putative interactions between protists and bacteria, or that both types of microbes in the termite gut follow shared structuring principles. Taken together, our results add to the notion that bacterial communities are more variable over evolutionary time than protist communities and might react more flexibly to changes in host ecology.

  20. Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species

    KAUST Repository

    Waidele, Lena

    2017-12-19

    The gut microbiome of lower termites comprises protists and bacteria that help these insects to digest cellulose and to thrive on wood. The composition of the termite gut microbiome correlates with phylogenetic distance of the animal host and host ecology (diet) in termites collected from their natural environment. However, carryover of transient microbes from host collection sites are an experimental concern and might contribute to the ecological imprints on the termite gut microbiome. Here, we set out to test whether an ecological imprint on the termite gut microbiome remains, when focusing on the persistent microbiome. Therefore, we kept five termite species under strictly controlled dietary conditions and subsequently profiled their protist and bacterial gut microbial communities using 18S and 16S rRNA gene amplicon sequencing. The species differed in their ecology; while three of the investigated species were wood-dwellers that feed on the piece of wood they live in and never leave except for the mating flight, the other two species were foragers that regularly leave their nests to forage for food. Despite these prominent ecological differences, protist microbiome structure aligned with phylogenetic relatedness of termite host species. Conversely, bacterial communities seemed more flexible, suggesting that microbiome structure aligned more strongly with the foraging and wood-dwelling ecologies. Interestingly, protist and bacterial community alpha-diversity correlated, suggesting either putative interactions between protists and bacteria, or that both types of microbes in the termite gut follow shared structuring principles. Taken together, our results add to the notion that bacterial communities are more variable over evolutionary time than protist communities and might react more flexibly to changes in host ecology.

  1. Yeast and bacterial diversity along a transect in an acidic, As-Fe rich environment revealed by cultural approaches.

    Science.gov (United States)

    Delavat, François; Lett, Marie-Claire; Lièvremont, Didier

    2013-10-01

    Acid mine drainages (AMDs) are often thought to harbour low biodiversity, yet little is known about the diversity distribution along the drainages. Using culture-dependent approaches, the microbial diversity from the Carnoulès AMD sediment was investigated for the first time along a transect showing progressive environmental stringency decrease. In total, 20 bacterial genera were detected, highlighting a higher bacterial diversity than previously thought. Moreover, this approach led to the discovery of 16 yeast species, demonstrating for the first time the presence of this important phylogenetic group in this AMD. All in all, the location of the microbes along the transect helps to better understand their distribution in a pollution gradient. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.

    2012-08-03

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.

  3. Nucleotide diversity analysis of three major bacterial blight resistance genes in rice.

    Directory of Open Access Journals (Sweden)

    Waikhom Bimolata

    Full Text Available Nucleotide sequence polymorphisms among R gene alleles influence the process of co-evolutionary interaction between host and pathogen by shaping the response of host plants towards invading pathogens. Here, we present the DNA sequence polymorphisms and diversities present among natural alleles of three rice bacterial blight resistance genes, Xa21, Xa26 and xa5. The diversity was examined across different wild relatives and cultivars of Oryza species. Functional significance of selected alleles was evaluated through semi-quantitative reverse transcription polymerase chain reaction and real time PCR. The greatest nucleotide diversity and singleton variable sites (SVS were present in Xa26 (π = 0.01958; SVS = 182 followed by xa5 and Xa21 alleles. The highest frequency of single nucleotide polymorphisms were observed in Xa21 alleles and least in xa5. Transition bias was observed in all the genes and 'G' to 'A' transitions were more favored than other form of transitions. Neutrality tests failed to show the presence of selection at these loci, though negative Tajima's D values indicate the presence of a rare form of polymorphisms. At the interspecies level, O. nivara exhibited more diversity than O. sativa. We have also identified two nearly identical resistant alleles of xa5 and two sequentially identical alleles of Xa21. The alleles of xa5 showed basal levels of expression while Xa21 alleles were functionally not expressed.

  4. Evaluation of the bacterial diversity of pressure ulcers using bTEFAP pyrosequencing.

    Science.gov (United States)

    Smith, Drake M; Snow, David E; Rees, Eric; Zischkau, Ann M; Hanson, J Delton; Wolcott, Randall D; Sun, Yan; White, Jennifer; Kumar, Shashi; Dowd, Scot E

    2010-09-21

    Decubitus ulcers, also known as bedsores or pressure ulcers, affect millions of hospitalized patients each year. The microflora of chronic wounds such as ulcers most commonly exist in the biofilm phenotype and have been known to significantly impair normal healing trajectories. Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP), a universal bacterial identification method, was used to identify bacterial populations in 49 decubitus ulcers. Diversity estimators were utilized and wound community compositions analyzed in relation to metadata such as Age, race, gender, and comorbidities. Decubitus ulcers are shown to be polymicrobial in nature with no single bacterium exclusively colonizing the wounds. The microbial community among such ulcers is highly variable. While there are between 3 and 10 primary populations in each wound there can be hundreds of different species present many of which are in trace amounts. There is no clearly significant differences in the microbial ecology of decubitus ulcer in relation to metadata except when considering diabetes. The microbial populations and composition in the decubitus ulcers of diabetics may be significantly different from the communities in non-diabetics. Based upon the continued elucidation of chronic wound bioburdens as polymicrobial infections, it is recommended that, in addition to traditional biofilm-based wound care strategies, an antimicrobial/antibiofilm treatment program can be tailored to each patient's respective wound microflora.

  5. Evaluation of the bacterial diversity of Pressure ulcers using bTEFAP pyrosequencing

    Directory of Open Access Journals (Sweden)

    Wolcott Randall D

    2010-09-01

    Full Text Available Abstract Background Decubitus ulcers, also known as bedsores or pressure ulcers, affect millions of hospitalized patients each year. The microflora of chronic wounds such as ulcers most commonly exist in the biofilm phenotype and have been known to significantly impair normal healing trajectories. Methods Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP, a universal bacterial identification method, was used to identify bacterial populations in 49 decubitus ulcers. Diversity estimators were utilized and wound community compositions analyzed in relation to metadata such as Age, race, gender, and comorbidities. Results Decubitus ulcers are shown to be polymicrobial in nature with no single bacterium exclusively colonizing the wounds. The microbial community among such ulcers is highly variable. While there are between 3 and 10 primary populations in each wound there can be hundreds of different species present many of which are in trace amounts. There is no clearly significant differences in the microbial ecology of decubitus ulcer in relation to metadata except when considering diabetes. The microbial populations and composition in the decubitus ulcers of diabetics may be significantly different from the communities in non-diabetics. Conclusions Based upon the continued elucidation of chronic wound bioburdens as polymicrobial infections, it is recommended that, in addition to traditional biofilm-based wound care strategies, an antimicrobial/antibiofilm treatment program can be tailored to each patient's respective wound microflora.

  6. Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts.

    Science.gov (United States)

    Webster, Nicole S; Taylor, Michael W; Behnam, Faris; Lücker, Sebastian; Rattei, Thomas; Whalan, Stephen; Horn, Matthias; Wagner, Michael

    2010-08-01

    Marine sponges contain complex bacterial communities of considerable ecological and biotechnological importance, with many of these organisms postulated to be specific to sponge hosts. Testing this hypothesis in light of the recent discovery of the rare microbial biosphere, we investigated three Australian sponges by massively parallel 16S rRNA gene tag pyrosequencing. Here we show bacterial diversity that is unparalleled in an invertebrate host, with more than 250,000 sponge-derived sequence tags being assigned to 23 bacterial phyla and revealing up to 2996 operational taxonomic units (95% sequence similarity) per sponge species. Of the 33 previously described 'sponge-specific' clusters that were detected in this study, 48% were found exclusively in adults and larvae - implying vertical transmission of these groups. The remaining taxa, including 'Poribacteria', were also found at very low abundance among the 135,000 tags retrieved from surrounding seawater. Thus, members of the rare seawater biosphere may serve as seed organisms for widely occurring symbiont populations in sponges and their host association might have evolved much more recently than previously thought. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

  7. The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition.

    Science.gov (United States)

    Heitlinger, Emanuel; Ferreira, Susana C M; Thierer, Dagmar; Hofer, Heribert; East, Marion L

    2017-01-01

    In mammals, two factors likely to affect the diversity and composition of intestinal bacteria (bacterial microbiome) and eukaryotes (eukaryome) are social status and age. In species in which social status determines access to resources, socially dominant animals maintain better immune processes and health status than subordinates. As high species diversity is an index of ecosystem health, the intestinal biome of healthier, socially dominant animals should be more diverse than those of subordinates. Gradual colonization of the juvenile intestine after birth predicts lower intestinal biome diversity in juveniles than adults. We tested these predictions on the effect of: (1) age (juvenile/adult) and (2) social status (low/high) on bacterial microbiome and eukaryome diversity and composition in the spotted hyena ( Crocuta crocuta ), a highly social, female-dominated carnivore in which social status determines access to resources. We comprehensively screened feces from 35 individually known adult females and 7 juveniles in the Serengeti ecosystem for bacteria and eukaryotes, using a set of 48 different amplicons (4 for bacterial 16S, 44 for eukaryote 18S) in a multi-amplicon sequencing approach. We compared sequence abundances to classical coprological egg or oocyst counts. For all parasite taxa detected in more than six samples, the number of sequence reads significantly predicted the number of eggs or oocysts counted, underscoring the value of an amplicon sequencing approach for quantitative measurements of parasite load. In line with our predictions, our results revealed a significantly less diverse microbiome in juveniles than adults and a significantly higher diversity of eukaryotes in high-ranking than low-ranking animals. We propose that free-ranging wildlife can provide an intriguing model system to assess the adaptive value of intestinal biome diversity for both bacteria and eukaryotes.

  8. Comparing the bacterial diversity of acute and chronic dental root canal infections.

    Directory of Open Access Journals (Sweden)

    Adriana L Santos

    Full Text Available This study performed barcoded multiplex pyrosequencing with a 454 FLX instrument to compare the microbiota of dental root canal infections associated with acute (symptomatic or chronic (asymptomatic apical periodontitis. Analysis of samples from 9 acute abscesses and 8 chronic infections yielded partial 16S rRNA gene sequences that were taxonomically classified into 916 bacterial species-level operational taxonomic units (OTUs (at 3% divergence belonging to 67 genera and 13 phyla. The most abundant phyla in acute infections were Firmicutes (52%, Fusobacteria (17% and Bacteroidetes (13%, while in chronic infections the dominant were Firmicutes (59%, Bacteroidetes (14% and Actinobacteria (10%. Members of Fusobacteria were much more prevalent in acute (89% than in chronic cases (50%. The most abundant/prevalent genera in acute infections were Fusobacterium and Parvimonas. Twenty genera were exclusively detected in acute infections and 18 in chronic infections. Only 18% (n = 165 of the OTUs at 3% divergence were shared by acute and chronic infections. Diversity and richness estimators revealed that acute infections were significantly more diverse than chronic infections. Although a high interindividual variation in bacterial communities was observed, many samples tended to group together according to the type of infection (acute or chronic. This study is one of the most comprehensive in-deep comparisons of the microbiota associated with acute and chronic dental root canal infections and highlights the role of diverse polymicrobial communities as the unit of pathogenicity in acute infections. The overall diversity of endodontic infections as revealed by the pyrosequencing technique was much higher than previously reported for endodontic infections.

  9. Bacterial diversity in Fe-rich hydrothermal sediments at two South Tonga Arc submarine volcanoes.

    Science.gov (United States)

    Forget, N L; Murdock, S A; Juniper, S K

    2010-12-01

    Seafloor iron oxide deposits are a common feature of submarine hydrothermal systems. Morphological study of these deposits has led investigators to suggest a microbiological role in their formation, through the oxidation of reduced Fe in hydrothermal fluids. Fe-oxidizing bacteria, including the recently described Zetaproteobacteria, have been isolated from a few of these deposits but generally little is known about the microbial diversity associated with this habitat. In this study, we characterized bacterial diversity in two Fe oxide samples collected on the seafloor of Volcanoes 1 and 19 on the South Tonga Arc. We were particularly interested in confirming the presence of Zetaproteobacteria at these two sites and in documenting the diversity of groups other than Fe oxidizers. Our results (small subunit rRNA gene sequence data) showed a surprisingly high bacterial diversity, with 150 operational taxonomic units belonging to 19 distinct taxonomic groups. Both samples were dominated by Zetaproteobacteria Fe oxidizers. This group was most abundant at Volcano 1, where sediments were richer in Fe and contained more crystalline forms of Fe oxides. Other groups of bacteria found at these two sites include known S- and a few N-metabolizing bacteria, all ubiquitous in marine environments. The low similarity of our clones with the GenBank database suggests that new species and perhaps new families were recovered. The results of this study suggest that Fe-rich hydrothermal sediments, while dominated by Fe oxidizers, can be exploited by a variety of autotrophic and heterotrophic micro-organisms. © 2010 Blackwell Publishing Ltd.

  10. Species richness in soil bacterial communities: a proposed approach to overcome sample size bias.

    Science.gov (United States)

    Youssef, Noha H; Elshahed, Mostafa S

    2008-09-01

    Estimates of species richness based on 16S rRNA gene clone libraries are increasingly utilized to gauge the level of bacterial diversity within various ecosystems. However, previous studies have indicated that regardless of the utilized approach, species richness estimates obtained are dependent on the size of the analyzed clone libraries. We here propose an approach to overcome sample size bias in species richness estimates in complex microbial communities. Parametric (Maximum likelihood-based and rarefaction curve-based) and non-parametric approaches were used to estimate species richness in a library of 13,001 near full-length 16S rRNA clones derived from soil, as well as in multiple subsets of the original library. Species richness estimates obtained increased with the increase in library size. To obtain a sample size-unbiased estimate of species richness, we calculated the theoretical clone library sizes required to encounter the estimated species richness at various clone library sizes, used curve fitting to determine the theoretical clone library size required to encounter the "true" species richness, and subsequently determined the corresponding sample size-unbiased species richness value. Using this approach, sample size-unbiased estimates of 17,230, 15,571, and 33,912 were obtained for the ML-based, rarefaction curve-based, and ACE-1 estimators, respectively, compared to bias-uncorrected values of 15,009, 11,913, and 20,909.

  11. Desulfovibrio bacterial species are increased in ulcerative colitis.

    LENUS (Irish Health Repository)

    Rowan, Fiachra

    2012-02-01

    BACKGROUND: Debate persists regarding the role of Desulfovibrio subspecies in ulcerative colitis. Combined microscopic and molecular techniques enable this issue to be investigated by allowing precise enumeration of specific bacterial species within the colonic mucous gel. The aim of this study was to combine laser capture microdissection and quantitative polymerase chain reaction to determine Desulfovibrio copy number in crypt-associated mucous gel in health and in acute and chronic ulcerative colitis. METHODS: Colonic mucosal biopsies were harvested from healthy controls (n = 19) and patients with acute (n = 10) or chronic (n = 10) ulcerative colitis. Crypt-associated mucous gel was obtained by laser capture microdissection throughout the colon. Pan-bacterial 16S rRNA and Desulfovibrio copy number\\/mm were obtained by polymerase chain reaction at each locus. Bacterial copy numbers were interrogated for correlation with location and disease activity. Data were evaluated using a combination of ordinary linear methods and linear mixed-effects models to cater for multiple interactions. RESULTS: Desulfovibrio positivity was significantly increased in acute and chronic ulcerative colitis at multiple levels within the colon, and after normalization with total bacterial signal, the relative Desulfovibrio load was increased in acute colitis compared with controls. Desulfovibrio counts did not significantly correlate with age, disease duration, or disease activity but interlevel correlations were found in adjacent colonic segments in the healthy control and chronic ulcerative colitis groups. CONCLUSION: The presence of Desulfovibrio subspecies is increased in ulcerative colitis and the data presented suggest that these bacteria represent an increased percentage of the colonic microbiome in acute ulcerative colitis.

  12. Soil bacterial diversity in degraded and restored lands of Northeast Brazil.

    Science.gov (United States)

    Araújo, Ademir Sérgio Ferreira; Borges, Clovis Daniel; Tsai, Siu Mui; Cesarz, Simone; Eisenhauer, Nico

    2014-11-01

    Land degradation deteriorates biological productivity and affects environmental, social, and economic sustainability, particularly so in the semi-arid region of Northeast Brazil. Although some studies exist reporting gross measures of soil microbial parameters and processes, limited information is available on how land degradation and restoration strategies influence the diversity and composition of soil microbial communities. In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. We found that land degradation decreased the diversity of soil bacteria as indicated by both reduced operational taxonomic unit (OTU) richness and Shannon index. Soils under native vegetation and restoration had significantly higher bacterial richness and diversity than degraded soils. Redundancy analysis revealed that low soil bacterial diversity correlated with a high respiratory quotient, indicating stressed microbial communities. By contrast, soil bacterial communities in restored land positively correlated with high soil P levels. Importantly, however, we found significant differences in the soil bacterial community composition under native vegetation and in restored land, which may indicate differences in their functioning despite equal levels of bacterial diversity.

  13. Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica.

    Science.gov (United States)

    Teixeira, Lia C R S; Peixoto, Raquel S; Cury, Juliano C; Sul, Woo Jun; Pellizari, Vivian H; Tiedje, James; Rosado, Alexandre S

    2010-08-01

    The Antarctic is a pristine environment that contributes to the maintenance of the global climate equilibrium. The harsh conditions of this habitat are fundamental to selecting those organisms able to survive in such an extreme habitat and able to support the relatively simple ecosystems. The DNA of the microbial community associated with the rhizospheres of Deschampsia antarctica Desv (Poaceae) and Colobanthus quitensis (Kunth) BartI (Caryophyllaceae), the only two native vascular plants that are found in Antarctic ecosystems, was evaluated using a 16S rRNA multiplex 454 pyrosequencing approach. This analysis revealed similar patterns of bacterial diversity between the two plant species from different locations, arguing against the hypothesis that there would be differences between the rhizosphere communities of different plants. Furthermore, the phylum distribution presented a peculiar pattern, with a bacterial community structure different from those reported of many other soils. Firmicutes was the most abundant phylum in almost all the analyzed samples, and there were high levels of anaerobic representatives. Also, some phyla that are dominant in most temperate and tropical soils, such as Acidobacteria, were rarely found in the analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Bifidobacterium (phylum Actinobacteria), Arcobacter (phylum Proteobacteria) and Faecalibacterium (phylum Firmicutes). To the best of our knowledge, this is the first major bacterial sequencing effort of this kind of soil, and it revealed more than expected diversity within these rhizospheres of both maritime Antarctica vascular plants in Admiralty Bay, King George Island, which is part of the South Shetlands archipelago.

  14. Diversity in protein glycosylation among insect species.

    Directory of Open Access Journals (Sweden)

    Gianni Vandenborre

    Full Text Available BACKGROUND: A very common protein modification in multicellular organisms is protein glycosylation or the addition of carbohydrate structures to the peptide backbone. Although the Class of the Insecta is the largest animal taxon on Earth, almost all information concerning glycosylation in insects is derived from studies with only one species, namely the fruit fly Drosophila melanogaster. METHODOLOGY/PRINCIPAL FINDINGS: In this report, the differences in glycoproteomes between insects belonging to several economically important insect orders were studied. Using GNA (Galanthus nivalis agglutinin affinity chromatography, different sets of glycoproteins with mannosyl-containing glycan structures were purified from the flour beetle (Tribolium castaneum, the silkworm (Bombyx mori, the honeybee (Apis mellifera, the fruit fly (D. melanogaster and the pea aphid (Acyrthosiphon pisum. To identify and characterize the purified glycoproteins, LC-MS/MS analysis was performed. For all insect species, it was demonstrated that glycoproteins were related to a broad range of biological processes and molecular functions. Moreover, the majority of glycoproteins retained on the GNA column were unique to one particular insect species and only a few glycoproteins were present in the five different glycoprotein sets. Furthermore, these data support the hypothesis that insect glycoproteins can be decorated with mannosylated O-glycans. CONCLUSIONS/SIGNIFICANCE: The results presented here demonstrate that oligomannose N-glycosylation events are highly specific depending on the insect species. In addition, we also demonstrated that protein O-mannosylation in insect species may occur more frequently than currently believed.

  15. Study of fecal bacterial diversity in Yunnan snub-nosed monkey ...

    African Journals Online (AJOL)

    Yomi

    The bacterial diversity in fecal samples from Yunnan snub-nosed monkey ... Based on the phylogenetic analysis, the fecal bacteria of R. bieti distributed ... and conservation genetics, but research on fecal bacterial ... The large number of microorganisms in the intestine of .... There was high evolutional relativity between.

  16. Impact of oil contamination and biostimulation on the diversity of indigenous bacterial communities in soil microcosms

    NARCIS (Netherlands)

    Evans, FF; Rosado, AS; Sebastian, GV; Casella, R; Machado, PLOA; Holmstrom, C; Kjelleberg, S; van Elsas, JD; Seldin, L

    2004-01-01

    The aim of this study was to analyse the effect of oil contamination and biostimulation (soil pH raise, and nitrogen, phosphate and sulphur addition) on the diversity of a bacterial community of an acidic Cambisol under Atlantic Forest. The experiment was based on the enumeration of bacterial

  17. Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates.

    Directory of Open Access Journals (Sweden)

    E Charlotte E Kvennefors

    Full Text Available BACKGROUND: Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral. METHODOLOGY/PRINCIPAL FINDINGS: Denaturing Gradient Gel Electrophoresis (DGGE of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by "White Syndrome" (WS underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome. CONCLUSIONS/SIGNIFICANCE: This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine

  18. Bacterial Communities in Malagasy Soils with Differing Levels of Disturbance Affecting Botanical Diversity

    Science.gov (United States)

    Blasiak, Leah C.; Schmidt, Alex W.; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Applequist, Wendy L.; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P.; Schmidt, Thomas M.; Hill, Russell T.

    2014-01-01

    Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas. PMID:24465484

  19. The effect of organic farming systems on species diversity

    Science.gov (United States)

    Leksono, Amin Setyo

    2017-11-01

    Organic farming systems have been well known to support the diversity of a wide range of taxa, including microorganisms, arable flora, invertebrates, birds, and mammals, which benefit from organic management leading to increases in abundance and/or species richness. The objective of this paper is to review the effect of organic farming on species diversity reported in several articles and compare this with the current study in Gondanglegi, Malang. A review of several studies showed that organic farming systems have been reported to increase species diversity, including that of mammals, birds, arthropods, vascular plants and arbuscular mycorrhizal fungi. The researchers about arthropod groups consisted of carabid beetles, butterflies, wasps, predators, and bees. Agricultural landscape, habitat type, farming system, landscape composition and connectivity all contribute to explaining species biodiversity and richness. Moreover, based on current and relevant studies, the results showed that the application of refugia blocks has increased arthropod diversity and composition.

  20. Does species diversity limit productivity in natural grassland communities?

    NARCIS (Netherlands)

    Grace, James B.; Anderson, T. Michael; Smith, Melinda D.; Seabloom, Eric; Andelman, Sandy J.; Meche, Gayna; Weiher, Evan; Allain, Larry K.; Jutila, Heli; Sankaran, Mahesh; Knops, Johannes; Ritchie, Mark; Willig, Michael R.

    Theoretical analyses and experimental studies of synthesized assemblages indicate that under particular circumstances species diversity can enhance community productivity through niche complementarity. It remains unclear whether this process has important effects in mature natural ecosystems where

  1. Bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP based assessment of prokaryotic diversity in metagenome of Lonar soda lake, India

    Directory of Open Access Journals (Sweden)

    Pravin Dudhagara

    2015-06-01

    Full Text Available Bacterial diversity and archaeal diversity in metagenome of the Lonar soda lake sediment were assessed by bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP. Metagenome comprised 5093 sequences with 2,531,282 bp and 53 ± 2% G + C content. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. PRJNA218849. Metagenome sequence represented the presence of 83.1% bacterial and 10.5% archaeal origin. A total of 14 different bacteria demonstrating 57 species were recorded with dominating species like Coxiella burnetii (17%, Fibrobacter intestinalis (12% and Candidatus Cloacamonas acidaminovorans (11%. Occurrence of two archaeal phyla representing 24 species, among them Methanosaeta harundinacea (35%, Methanoculleus chikugoensis (12% and Methanolinea tarda (11% were dominating species. Significant presence of 11% sequences as an unclassified indicated the possibilities for unknown novel prokaryotes from the metagenome.

  2. Bacterial diversity in different regions of gastrointestinal tract of Giant African snail (Achatina fulica).

    Science.gov (United States)

    Pawar, Kiran D; Banskar, Sunil; Rane, Shailendra D; Charan, Shakti S; Kulkarni, Girish J; Sawant, Shailesh S; Ghate, Hemant V; Patole, Milind S; Shouche, Yogesh S

    2012-12-01

    The gastrointestinal (GI) tract of invasive land snail Achatina fulica is known to harbor metabolically active bacterial communities. In this study, we assessed the bacterial diversity in the different regions of GI tract of Giant African snail, A. fulica by culture-independent and culture-dependent methods. Five 16S rRNA gene libraries from different regions of GI tract of active snails indicated that sequences affiliated to phylum γ-Proteobacteria dominated the esophagus, crop, intestine, and rectum libraries, whereas sequences affiliated to Tenericutes dominated the stomach library. On phylogenetic analysis, 30, 27, 9, 27, and 25 operational taxonomic units (OTUs) from esophagus, crop, stomach, intestine, and rectum libraries were identified, respectively. Estimations of the total bacterial diversity covered along with environmental cluster analysis showed highest bacterial diversity in the esophagus and lowest in the stomach. Thirty-three distinct bacterial isolates were obtained, which belonged to 12 genera of two major bacterial phyla namely γ-Proteobacteria and Firmicutes. Among these, Lactococcus lactis and Kurthia gibsonii were the dominant bacteria present in all GI tract regions. Quantitative real-time polymerase chain reaction (qPCR) analysis indicated significant differences in bacterial load in different GI tract regions of active and estivating snails. The difference in the bacterial load between the intestines of active and estivating snail was maximum. Principal component analysis (PCA) of terminal restriction fragment length polymorphism suggested that bacterial community structure changes only in intestine when snail enters estivation state. © 2012 The Authors. Published by Blackwell Publishing Ltd.

  3. Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species

    Science.gov (United States)

    Merino, Enrique; Bonomi, Hernán Ruy; Goldbaum, Fernando Alberto; García-Angulo, Víctor Antonio

    2015-01-01

    Riboflavin, the precursor for the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide, is an essential metabolite in all organisms. While the functions for de novo riboflavin biosynthesis and riboflavin import may coexist in bacteria, the extent of this co-occurrence is undetermined. The RibM, RibN, RfuABCD and the energy-coupling factor-RibU bacterial riboflavin transporters have been experimentally characterized. In addition, ImpX, RfnT and RibXY are proposed as riboflavin transporters based on positional clustering with riboflavin biosynthetic pathway (RBP) genes or conservation of the FMN riboswitch regulatory element. Here, we searched for the FMN riboswitch in bacterial genomes to identify genes encoding riboflavin transporters and assessed their distribution among bacteria. Two new putative riboflavin transporters were identified: RibZ in Clostridium and RibV in Mesoplasma florum. Trans-complementation of an Escherichia coli riboflavin auxotroph strain confirmed the riboflavin transport activity of RibZ from Clostridium difficile, RibXY from Chloroflexus aurantiacus, ImpX from Fusobacterium nucleatum and RfnT from Ochrobactrum anthropi. The analysis of the genomic distribution of all known bacterial riboflavin transporters revealed that most occur in species possessing the RBP and that some bacteria may even encode functional riboflavin transporters from two different families. Our results indicate that some species possess ancestral riboflavin transporters, while others possess transporters that appear to have evolved recently. Moreover, our data suggest that unidentified riboflavin transporters also exist. The present study doubles the number of experimentally characterized riboflavin transporters and suggests a specific, non-accessory role for these proteins in riboflavin-prototrophic bacteria. PMID:25938806

  4. Investigation of the bacterial communities associated with females of Lutzomyia sand fly species from South America.

    Directory of Open Access Journals (Sweden)

    Mauricio R V Sant'Anna

    Full Text Available Phlebotomine sand flies are vectors of Leishmania that are acquired by the female sand fly during blood feeding on an infected mammal. Leishmania parasites develop exclusively in the gut lumen during their residence in the insect before transmission to a suitable host during the next blood feed. Female phlebotomine sand flies are blood feeding insects but their life style of visiting plants as well as animals, and the propensity for larvae to feed on detritus including animal faeces means that the insect host and parasite are exposed to a range of microorganisms. Thus, the sand fly microbiota may interact with the developing Leishmania population in the gut. The aim of the study was to investigate and identify the bacterial diversity associated with wild adult female Lutzomyia sand flies from different geographical locations in the New World. The bacterial phylotypes recovered from 16S rRNA gene clone libraries obtained from wild caught adult female Lutzomyia sand flies were estimated from direct band sequencing after denaturing gradient gel electrophoresis of bacterial 16 rRNA gene fragments. These results confirm that the Lutzomyia sand flies contain a limited array of bacterial phylotypes across several divisions. Several potential plant-related bacterial sequences were detected including Erwinia sp. and putative Ralstonia sp. from two sand fly species sampled from 3 geographically separated regions in Brazil. Identification of putative human pathogens also demonstrated the potential for sand flies to act as vectors of bacterial pathogens of medical importance in addition to their role in Leishmania transmission.

  5. Diversity of bacterial communities on the facial skin of different age-group Thai males.

    Science.gov (United States)

    Wilantho, Alisa; Deekaew, Pamornya; Srisuttiyakorn, Chutika; Tongsima, Sissades; Somboonna, Naraporn

    2017-01-01

    , revealed differences in the distribution pattern of species, although common bacteria were present in both biogeographical samples. Furthermore, B-RISA served as a crosscheck result to the 16S rRNA gene sequencing (i.e., differences between teenage and elderly microbiota). This study revealed and compared the microbial diversity on different aged Thai male faces, and included analyses for representing the bacterial flora, the clinical skin characteristics, and comparison with the US age-matched. The results represent the first skin microbiota of Thai males, and helps the design of a large-scale skin microbiome study of Thais. The findings of the diversity among ages, skin type and national biogeography supported the importance of these traits in the skin microbiome and in developing a safe and sustainable treatment for acne and aging skin diseases.

  6. Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus microplus through tag-encoded pyrosequencing

    Directory of Open Access Journals (Sweden)

    Bendele Kylie G

    2011-01-01

    Full Text Available Abstract Background Ticks are regarded as the most relevant vectors of disease-causing pathogens in domestic and wild animals. The cattle tick, Rhipicephalus (Boophilus microplus, hinders livestock production in tropical and subtropical parts of the world where it is endemic. Tick microbiomes remain largely unexplored. The objective of this study was to explore the R. microplus microbiome by applying the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP technique to characterize its bacterial diversity. Pyrosequencing was performed on adult males and females, eggs, and gut and ovary tissues from adult females derived from samples of R. microplus collected during outbreaks in southern Texas. Results Raw data from bTEFAP were screened and trimmed based upon quality scores and binned into individual sample collections. Bacteria identified to the species level include Staphylococcus aureus, Staphylococcus chromogenes, Streptococcus dysgalactiae, Staphylococcus sciuri, Serratia marcescens, Corynebacterium glutamicum, and Finegoldia magna. One hundred twenty-one bacterial genera were detected in all the life stages and tissues sampled. The total number of genera identified by tick sample comprised: 53 in adult males, 61 in adult females, 11 in gut tissue, 7 in ovarian tissue, and 54 in the eggs. Notable genera detected in the cattle tick include Wolbachia, Coxiella, and Borrelia. The molecular approach applied in this study allowed us to assess the relative abundance of the microbiota associated with R. microplus. Conclusions This report represents the first survey of the bacteriome in the cattle tick using non-culture based molecular approaches. Comparisons of our results with previous bacterial surveys provide an indication of geographic variation in the assemblages of bacteria associated with R. microplus. Additional reports on the identification of new bacterial species maintained in nature by R. microplus that may be

  7. Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing

    Science.gov (United States)

    2011-01-01

    Background Ticks are regarded as the most relevant vectors of disease-causing pathogens in domestic and wild animals. The cattle tick, Rhipicephalus (Boophilus) microplus, hinders livestock production in tropical and subtropical parts of the world where it is endemic. Tick microbiomes remain largely unexplored. The objective of this study was to explore the R. microplus microbiome by applying the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) technique to characterize its bacterial diversity. Pyrosequencing was performed on adult males and females, eggs, and gut and ovary tissues from adult females derived from samples of R. microplus collected during outbreaks in southern Texas. Results Raw data from bTEFAP were screened and trimmed based upon quality scores and binned into individual sample collections. Bacteria identified to the species level include Staphylococcus aureus, Staphylococcus chromogenes, Streptococcus dysgalactiae, Staphylococcus sciuri, Serratia marcescens, Corynebacterium glutamicum, and Finegoldia magna. One hundred twenty-one bacterial genera were detected in all the life stages and tissues sampled. The total number of genera identified by tick sample comprised: 53 in adult males, 61 in adult females, 11 in gut tissue, 7 in ovarian tissue, and 54 in the eggs. Notable genera detected in the cattle tick include Wolbachia, Coxiella, and Borrelia. The molecular approach applied in this study allowed us to assess the relative abundance of the microbiota associated with R. microplus. Conclusions This report represents the first survey of the bacteriome in the cattle tick using non-culture based molecular approaches. Comparisons of our results with previous bacterial surveys provide an indication of geographic variation in the assemblages of bacteria associated with R. microplus. Additional reports on the identification of new bacterial species maintained in nature by R. microplus that may be pathogenic to its vertebrate hosts

  8. Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity.

    Science.gov (United States)

    Jurasinski, Gerald; Retzer, Vroni; Beierkuhnlein, Carl

    2009-02-01

    Almost half a century after Whittaker (Ecol Monogr 30:279-338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative--depending on the organism(s) or ecosystems investigated--this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term "inventory diversity." Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness ("key concept" vs. "abstruse concept"). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, "differentiation diversity" (first group) and "proportional diversity" (second group). Thus, we propose to use the terms "inventory diversity" for within-sample diversity, "differentiation diversity" for compositional similarity between samples, and "proportional diversity" for the

  9. Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil.

    Science.gov (United States)

    Lynn, Tin Mar; Liu, Qiong; Hu, Yajun; Yuan, Hongzhao; Wu, Xiaohong; Khai, Aye Aye; Wu, Jinshui; Ge, Tida

    2017-07-01

    Studying shifts in microbial communities under different land use can help in determining the impact of land use on microbial diversity. In this study, we analyzed four different land-use types to determine their bacterial and archaeal diversity and abundance. Three natural ecosystems, that is, wetland (WL), grassland (GL), and forest (FR) soils, and one agricultural soil, that is, tea plantation (TP) soil, were investigated to determine how land use shapes bacterial and archaeal diversity. For this purpose, molecular analyses, such as quantitative polymerase chain reaction (Q-PCR), 16S rRNA gene sequencing, and terminal restriction fragment length polymorphism (T-RFLP), were used. Soil physicochemical properties were determined, and statistical analyses were performed to identify the key factors affecting microbial diversity in these soils. Phylogenetic affiliations determined using the Ribosomal Database Project (RDP) database and T-RFLP revealed that the soils had differing bacterial diversity. WL soil was rich in only Proteobacteria, whereas GR soil was rich in Proteobacteria, followed by Actinobacteria. FR soil had higher abundance of Chloroflexi species than these soils. TP soil was rich in Actinobacteria, followed by Chloroflexi, Acidobacteria, Proteobacteria, and Firmicutes. The archaeal diversity of GL and FR soils was similar in that most of their sequences were closely related to Nitrososphaerales (Thaumarchaeota phylum). In contrast, WL soil, followed by TP soil, had greater archaeal diversity than other soils. Eight different archaeal classes were found in WL soil, and Pacearchaeota class was the richest one. The abundance of bacterial and archaeal 16S rRNA gene copies in WL and GL soils was significantly higher than that in FR and TP soils. Redundancy analysis showed that bacterial diversity was influenced by abiotic factors, e.g., total organic carbon and pH, whereas total nitrogen, pH, and cation exchange capacity (CEC) significantly affected

  10. Ubiquity and diversity of heterotrophic bacterial nasA genes in diverse marine environments.

    Directory of Open Access Journals (Sweden)

    Xuexia Jiang

    Full Text Available Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB. In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III. Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating

  11. Stability of chloroquine phosphate tablets inoculated with bacterial species

    International Nuclear Information System (INIS)

    Obuekwe, I.F.; Orhe, C.A.; Iwaagu, M.U.

    2003-01-01

    Five popular brands of chloroquine tablets available to the average Nigerian consumers were examined for the effects of Staphylococcus aureus and Bacillus cereus, on the dissolution, disintegration and hardness after six weeks of incubation. The maximum percent dissolution was 98.34% with bacillus subtilis while the minimum was 19.12% with staphylococcus aureus. The disintegration results showed a maximum of 69 min. 19 sec with Staphylococcus aureus while the least was 56 sec with Bacillus subtilis. The maximum hardness obtained was 12.75 kg and the least was 1.25 kg also with Staphylococcus aureus. The dissolution, disintegration and hardness also varied with the control. The metabolic activities of the bacterial species were believed to have caused the variations in the physical properties of the chloroquine phosphate tablets. The results from this investigation strongly advises adequate storage of chloroquine phosphate tablets, especially when it is the drug of choice for the of sub-Saharan Africa. (author)

  12. Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

    Science.gov (United States)

    Ding, Tao; Melcher, Ulrich

    2016-01-01

    Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

  13. Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

    Directory of Open Access Journals (Sweden)

    Tao Ding

    Full Text Available Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

  14. Diversity of the Cryptococcus neoformans-Cryptococcus gattii species complex.

    NARCIS (Netherlands)

    Bovers, M.; Hagen, F.; Boekhout, T.

    2008-01-01

    More than 110 years of study of the Cryptococcus neoformans and Cryptococcus gattii species complex has resulted in an enormous accumulation of fundamental and applied biological and clinical knowledge. Recent developments in our understanding of the diversity within the species complex are

  15. Towards conserving regional mammalian species diversity: a case ...

    African Journals Online (AJOL)

    1995-03-03

    Mar 3, 1995 ... Species richness maps were derived for the Transvaal region from two different databases, namely a primary point database based on ... of biological diversity is internationally supported, there is no agreement on the ..... example is that of the Rodentia. where greatest species diver- sity. based on survey ...

  16. Species Diversity and Growth Forms in Tropical American Palm Communities

    DEFF Research Database (Denmark)

    Balslev, Henrik; Kahn, Francis; Millán, Betty

    2011-01-01

    To advance our understanding of the processes that govern the assembly of palm communities and the local coexistence of numerous palm species, we here synthesize available information in the literature on species diversity and growth-form composition in palm communities across the Americas. Ameri...

  17. Species and Scale Dependence of Bacterial Motion Dynamics

    Science.gov (United States)

    Sund, N. L.; Yang, X.; Parashar, R.; Plymale, A.; Hu, D.; Kelly, R.; Scheibe, T. D.

    2017-12-01

    Many metal reducing bacteria are motile with their motion characteristics described by run-and-tumble behavior exhibiting series of flights (jumps) and waiting (residence) time spanning a wide range of values. Accurate models of motility allow for improved design and evaluation of in-situ bioremediation in the subsurface. While many bioremediation models neglect the motion of the bacteria, others treat motility using an advection dispersion equation, which assumes that the motion of the bacteria is Brownian.The assumption of Brownian motion to describe motility has enormous implications on predictive capabilities of bioremediation models, yet experimental evidence of this assumption is mixed [1][2][3]. We hypothesize that this is due to the species and scale dependence of the motion dynamics. We test our hypothesis by analyzing videos of motile bacteria of five different species in open domains. Trajectories of individual cells ranging from several seconds to few minutes in duration are extracted in neutral conditions (in the absence of any chemical gradient). The density of the bacteria is kept low so that the interaction between the bacteria is minimal. Preliminary results show a transition from Fickian (Brownian) to non-Fickian behavior for one species of bacteria (Pelosinus) and persistent Fickian behavior of another species (Geobacter).Figure: Video frames of motile bacteria with the last 10 seconds of their trajectories drawn in red. (left) Pelosinus and (right) Geobacter.[1] Ariel, Gil, et al. "Swarming bacteria migrate by Lévy Walk." Nature Communications 6 (2015).[2] Saragosti, Jonathan, Pascal Silberzan, and Axel Buguin. "Modeling E. coli tumbles by rotational diffusion. Implications for chemotaxis." PloS one 7.4 (2012): e35412.[3] Wu, Mingming, et al. "Collective bacterial dynamics revealed using a three-dimensional population-scale defocused particle tracking technique." Applied and Environmental Microbiology 72.7 (2006): 4987-4994.

  18. Endophytic bacterial diversity in banana 'Prata Anã' (Musa spp. roots

    Directory of Open Access Journals (Sweden)

    Suzane A. Souza

    2013-01-01

    Full Text Available The genetic diversity of endophytic bacteria in banana 'Prata Anã' roots was characterized. Two hundred and one endophytic bacteria were isolated, 151 of which were classified as Gram-positive and 50 as Gram-negative. No hypersensitivity response was observed in any of the isolates. The rep-PCR technique generated different molecular profiles for each primer set (REP, ERIC and BOX. Fifty readable loci were obtained and all of the fragments were polymorphic. Amplified ribosomal DNA restriction analysis (ARDRA of the isolates based on cleavage with four restriction enzymes yielded 45 polymorphic bands and no monomorphic bands. PCR amplified the nifH gene in 24 isolates. 16S rDNA sequencing of the 201 bacterial isolates yielded 102 high-quality sequences. Sequence analyses revealed that the isolates were distributed among ten bacterial genera (Agrobacterium, Aneurinibacillus, Bacillus, Enterobacter, Klebsiella, Lysinibacillus, Micrococcus, Paenibacillus, Rhizobium and Sporolactobacillus and included 15 species. The greatest number of isolates belonged to the genus Bacillus. The bacteria identified in this study may be involved in promoting growth, phosphate solubilization, biological control and nitrogen fixation in bananas.

  19. Analysis of bacterial genetic diversity in biofloc by using ARDRA 16S-rRNA gene

    Directory of Open Access Journals (Sweden)

    , Widanarni

    2015-05-01

    Full Text Available ABSTRACT This study aimed to analyze the genetic diversity of bacteria associated in bioflocs using 16S-rRNA polymerase chain reaction (PCR with ARDRA technique. A total of 38 dominant bacterial isolates was obtained from bioflocs samples and of these isolates, 16S-rRNA gene was then isolated and amplified using PCR. The 16S-rRNA gene of the isolates was then cut using HaeIII (5’-GG↓CC and HhaI (5’-GCG↓C restriction enzymes resulting an ARDRA pattern which was further used as the binary data for the construction of phylogenetics tree that was used to estimate the group of bacteria. The result with HaeIII cut restriction enzyme from biofloc-associated bacteria gave 11 ARDRA patterns, while with the restriction enzyme HhaI gave eight ARDRA patterns. Phylogenetics of bacterial populations from biofloc-based cultivation system water consisted of at least 13 different bacterial species. Result of sequencing from two gene sample 16S-rRNA were identified as Microbacterium foliorumand and Pseudomonas putida. Keywords: bacterial diversity, ARDRA, biofloc, phylogeny  ABSTRAK Penelitian ini bertujuan untuk menganalisis keragaman genetika bakteri bioflok menggunakan metode polymerase chain reaction (PCR 16S-rRNA dengan teknik ARDRA. Sebanyak 38 isolat bakteri dominan yang diperoleh diamplifikasi gen 16S-rRNAnya dengan PCR, kemudian dipotong dengan enzim restriksi HaeIII (5’-GG↓CC dan HhaI (5’-GCG↓C. Pola ARDRA ini dijadikan data biner sebagai input untuk konstruksi pohon filogenetika yang dapat digunakan untuk memerkirakan jenis bakteri yang ada. Gen 16S-rRNA hasil PCR setelah dipotong dengan enzim restriksi HaeIII didapatkan 11 pola ARDRA, sedangkan dengan enzim restriksi HhaI menghasilkan delapan pola ARDRA. Berdasarkan pohon filogenetika, diketahui populasi bakteri pada air sistem budidaya bioflok sedikitnya terdiri atas 13 jenis bakteri. Berdasarkan sekuensing dari dua sampel gen 16S-rRNA teridentifikasi jenis bakteri Microbacterium

  20. Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure.

    Science.gov (United States)

    Ishaq, Suzanne L; Johnson, Stephen P; Miller, Zach J; Lehnhoff, Erik A; Olivo, Sarah; Yeoman, Carl J; Menalled, Fabian D

    2017-02-01

    Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition.

  1. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

    Science.gov (United States)

    Pearson, T.; Giffard, P.; Beckstrom-Sternberg, S.; Auerbach, R.; Hornstra, H.; Tuanyok, A.; Price, E.P.; Glass, M.B.; Leadem, B.; Beckstrom-Sternberg, J. S.; Allan, G.J.; Foster, J.T.; Wagner, D.M.; Okinaka, R.T.; Sim, S.H.; Pearson, O.; Wu, Z.; Chang, J.; Kaul, R.; Hoffmaster, A.R.; Brettin, T.S.; Robison, R.A.; Mayo, M.; Gee, J.E.; Tan, P.; Currie, B.J.; Keim, P.

    2009-01-01

    Background: Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results: Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion: We describe an

  2. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

    Directory of Open Access Journals (Sweden)

    Kaul Rajinder

    2009-11-01

    Full Text Available Abstract Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia

  3. Bacterial diversity in agricultural soils during litter decomposition

    NARCIS (Netherlands)

    Dilly, O.; Bloem, J.; Vos, A.; Munch, J.C.

    2004-01-01

    Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band.

  4. Bacterial diversity of oil palm Elaeis guineensis basal stems

    Science.gov (United States)

    Amran, Afzufira; Jangi, Mohd Sanusi; Aqma, Wan Syaidatul; Yusof, Nurul Yuziana Mohd; Bakar, Mohd Faizal Abu; Isa, Mohd Noor Mat

    2016-11-01

    Oil palm, Elaeis guineensis is one of the major industrial production crops in Malaysia. Basal stem rot, caused by the white fungus, Ganoderma boninense, is a disease that reduces oil palm yields in most production areas of the world. Understanding of bacterial community that is associated with Ganoderma infection will shed light on how this bacterial community contributes toward the severity of the infection. In this preliminary study, we assessed the bacterial community that inhabit the basal stems of E. guineensis based on 16S rRNA gene as a marker using next generation sequencing platform. This result showed that a total of 84,372 operational taxonomic-units (OTUs) were identified within six samples analyzed. A total 55,049 OTUs were assigned to known taxonomy whereas 29,323 were unassigned. Cyanobacteria, Bacteroidetes, Firmicutes and Proteobacteria were the most abundant phyla found in all six samples and the unique taxonomy assigned for each infected and healthy samples were also identified. The findings from this study will further enhance our knowledge in the interaction of bacterial communities against Ganoderma infection within the oil palm host plant and for a better management of the basal stems rot disease.

  5. Satellite lakes as reservoirs of fish species diversity

    OpenAIRE

    Nkalubo, W.; Wandera, S.B.; Namulemo, G.

    2010-01-01

    Satellite lakes and rivers in the Victoria and Kyoga basins provide a sanctuary for endangered native fish species. The structural heterogeneity of macrophyte covering these lakes has made it possible for most of the biodiversity to be kept intact. The Kyoga minor lakes have the highest fish species diversity especially of the haplochromines. Most fish communities of these satellite lakes are composed of native species.

  6. REVIEW: The Diversity of Indigenous Honey Bee Species of Indonesia

    Directory of Open Access Journals (Sweden)

    SOESILAWATI HADISOESILO

    2001-01-01

    Full Text Available It has been known that Indonesia has the most diverse honey bee species in the world. At least five out of nine species of honey bees are native to Indonesia namely Apis andreniformis, A. dorsata, A. cerana, A. koschevnikovi, and A. nigrocincta. One species, A. florea, although it was claimed to be a species native to Indonesia, it is still debatable whether it is really found in Indonesia or not. The new species, A. nuluensis, which is found in Sabah, Borneo is likely to be found in Kalimantan but it has not confirmed yet. This paper discusses briefly the differences among those native honey bees.

  7. Remote sensing of species diversity using Landsat 8 spectral variables

    Science.gov (United States)

    Madonsela, Sabelo; Cho, Moses Azong; Ramoelo, Abel; Mutanga, Onisimo

    2017-11-01

    The application of remote sensing in biodiversity estimation has largely relied on the Normalized Difference Vegetation Index (NDVI). The NDVI exploits spectral information from red and near infrared bands of Landsat images and it does not consider canopy background conditions hence it is affected by soil brightness which lowers its sensitivity to vegetation. As such NDVI may be insufficient in explaining tree species diversity. Meanwhile, the Landsat program also collects essential spectral information in the shortwave infrared (SWIR) region which is related to plant properties. The study was intended to: (i) explore the utility of spectral information across Landsat-8 spectrum using the Principal Component Analysis (PCA) and estimate alpha diversity (α-diversity) in the savannah woodland in southern Africa, and (ii) define the species diversity index (Shannon (H‧), Simpson (D2) and species richness (S) - defined as number of species in a community) that best relates to spectral variability on the Landsat-8 Operational Land Imager dataset. We designed 90 m × 90 m field plots (n = 71) and identified all trees with a diameter at breast height (DbH) above 10 cm. H‧, D2 and S were used to quantify tree species diversity within each plot and the corresponding spectral information on all Landsat-8 bands were extracted from each field plot. A stepwise linear regression was applied to determine the relationship between species diversity indices (H‧, D2 and S) and Principal Components (PCs), vegetation indices and Gray Level Co-occurrence Matrix (GLCM) texture layers with calibration (n = 46) and test (n = 23) datasets. The results of regression analysis showed that the Simple Ratio Index derivative had a higher relationship with H‧, D2 and S (r2= 0.36; r2= 0.41; r2= 0.24 respectively) compared to NDVI, EVI, SAVI or their derivatives. Moreover the Landsat-8 derived PCs also had a higher relationship with H‧ and D2 (r2 of 0.36 and 0.35 respectively) than the

  8. Diverse microbial species survive high ammonia concentrations

    Science.gov (United States)

    Kelly, Laura C.; Cockell, Charles S.; Summers, Stephen

    2012-04-01

    Planetary protection regulations are in place to control the contamination of planets and moons with terrestrial micro-organisms in order to avoid jeopardizing future scientific investigations relating to the search for life. One environmental chemical factor of relevance in extraterrestrial environments, specifically in the moons of the outer solar system, is ammonia (NH3). Ammonia is known to be highly toxic to micro-organisms and may disrupt proton motive force, interfere with cellular redox reactions or cause an increase of cell pH. To test the survival potential of terrestrial micro-organisms exposed to such cold, ammonia-rich environments, and to judge whether current planetary protection regulations are sufficient, soil samples were exposed to concentrations of NH3 from 5 to 35% (v/v) at -80°C and room temperature for periods up to 11 months. Following exposure to 35% NH3, diverse spore-forming taxa survived, including representatives of the Firmicutes (Bacillus, Sporosarcina, Viridibacillus, Paenibacillus, Staphylococcus and Brevibacillus) and Actinobacteria (Streptomyces). Non-spore forming organisms also survived, including Proteobacteria (Pseudomonas) and Actinobacteria (Arthrobacter) that are known to have environmentally resistant resting states. Clostridium spp. were isolated from the exposed soil under anaerobic culture. High NH3 was shown to cause a reduction in viability of spores over time, but spore morphology was not visibly altered. In addition to its implications for planetary protection, these data show that a large number of bacteria, potentially including spore-forming pathogens, but also environmentally resistant non-spore-formers, can survive high ammonia concentrations.

  9. Microbial diversity in the floral nectar of seven Epipactis (Orchidaceae) species

    Science.gov (United States)

    Jacquemyn, Hans; Lenaerts, Marijke; Tyteca, Daniel; Lievens, Bart

    2013-01-01

    Abstract Floral nectar of animal-pollinated plants is commonly infested with microorganisms, yet little is known about the microorganisms inhabiting the floral nectar of orchids. In this study, we investigated microbial communities occurring in the floral nectar of seven Epipactis (Orchidaceae) species. Culturable bacteria and yeasts were isolated and identified by partially sequencing the small subunit (SSU) ribosomal RNA (rRNA) gene and the D1/D2 domains of the large subunit (LSU) rRNA gene, respectively. Using three different culture media, we found that bacteria were common inhabitants of the floral nectar of Epipactis. The most widely distributed bacterial operational taxonomic units (OTUs) in nectar of Epipactis were representatives of the family of Enterobacteriaceae, with an unspecified Enterobacteriaceae bacterium as the most common. In contrast to previous studies investigating microbial communities in floral nectar, very few yeast species (mainly of the genus Cryptococcus) were observed, and most of them occurred in very low densities. Total OTU richness (i.e., the number of bacterial and yeast OTUs per orchid species) varied between 4 and 20. Cluster analysis revealed that microbial communities of allogamous species differed from those of autogamous and facultatively autogamous species. This study extends previous efforts to identify microbial communities in floral nectar and indicates that the floral nectar of the orchids investigated mainly contained bacterial communities with moderate phylogenetic diversity. PMID:23836678

  10. Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities

    Directory of Open Access Journals (Sweden)

    Kristin Aleklett

    2015-02-01

    Full Text Available Plant roots are known to harbor large and diverse communities of bacteria. It has been suggested that plant identity can structure these root-associated communities, but few studies have specifically assessed how the composition of root microbiota varies within and between plant species growing under natural conditions. We assessed the community composition of endophytic and epiphytic bacteria through high throughput sequencing using 16S rDNA derived from root tissues collected from a population of a wild, clonal plant (Orange hawkweed–Pilosella aurantiaca as well as two neighboring plant species (Oxeye daisy–Leucanthemum vulgare and Alsike clover–Trifolium hybridum. Our first goal was to determine if plant species growing in close proximity, under similar environmental conditions, still hosted unique root microbiota. Our results showed that plants of different species host distinct bacterial communities in their roots. In terms of community composition, Betaproteobacteria (especially the family Oxalobacteraceae were found to dominate in the root microbiota of L. vulgare and T. hybridum samples, whereas the root microbiota of P. aurantiaca had a more heterogeneous distribution of bacterial abundances where Gammaproteobacteria and Acidobacteria occupied a larger portion of the community. We also explored the extent of individual variance within each plant species investigated, and found that in the plant species thought to have the least genetic variance among individuals (P. aurantiaca still hosted just as diverse microbial communities. Whether all plant species host their own distinct root microbiota and plants more closely related to each other share more similar bacterial communities still remains to be fully explored, but among the plants examined in this experiment there was no trend that the two species belonging to the same family shared more similarities in terms of bacterial community composition.

  11. Rare species support vulnerable functions in high-diversity ecosystems.

    Science.gov (United States)

    Mouillot, David; Bellwood, David R; Baraloto, Christopher; Chave, Jerome; Galzin, Rene; Harmelin-Vivien, Mireille; Kulbicki, Michel; Lavergne, Sebastien; Lavorel, Sandra; Mouquet, Nicolas; Paine, C E Timothy; Renaud, Julien; Thuiller, Wilfried

    2013-01-01

    Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across

  12. Rare species support vulnerable functions in high-diversity ecosystems.

    Directory of Open Access Journals (Sweden)

    David Mouillot

    Full Text Available Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees, we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by

  13. Bacterial diversity in goat milk from the Guanzhong area of China.

    Science.gov (United States)

    Zhang, Fuxin; Wang, Zhaoxia; Lei, Feiyan; Wang, Bini; Jiang, Shuaiming; Peng, Qiannan; Zhang, Jiachao; Shao, Yuyu

    2017-10-01

    In this study, the V3 and V4 regions of the 16S rRNA gene from metagenomic DNA were sequenced to identify differences in microbial diversity in raw milk of Saanen and Guanzhong goats from the Guanzhong area of China. The results showed that Proteobacteria was the predominant phylum, accounting for 71.31% of all phyla identified in milk from the 2 breeds, and Enterobacter was the predominant genus (24.69%) within the microbial community. Microbial alpha diversity from Saanen goat milk was significantly higher than that of Guanzhong goat milk based on bioinformatic analysis of indices of Chao1, Shannon, Simpson, observed species, and the abundance-based coverage estimator. Functional genes and their likely metabolic pathways were predicted, which demonstrated that the functional genes present in the bacteria in goat milk were enriched in pathways for amino acid metabolism and carbohydrate metabolism, which represented 11.93 and 11.23% of functional genes, respectively. Physicochemical properties such as pH, protein, fat, and AA levels were also determined and correlations made with microbial diversity. We detected a significant difference in the content of lactose and 6 AA, which were higher in Saanen milk than in Guanzhong milk, and positively correlated with microbial carbohydrate metabolism and AA metabolism. Lactococcus, Lactobacillus, Bifidobacterium, Enterococcus, and Streptococcus, which are lactose-utilizing genera, were more abundant in Saanen milk than in Guanzhong milk. Higher levels of lactose in Saanen goat milk may explain its greater microbial diversity. We also demonstrated that most of the AA metabolism-related bacterial genera (e.g., Massilia, Bacteroides, Lysobacter) were enriched in Saanen goat milk. In this research, both probiotic and pathogenic bacteria were identified in goat milk, which provided the microbial information necessary to direct the utilization of beneficial microbial resources and prevent the development of harmful organisms in

  14. Tree species diversity promotes aboveground carbon storage through functional diversity and functional dominance.

    Science.gov (United States)

    Mensah, Sylvanus; Veldtman, Ruan; Assogbadjo, Achille E; Glèlè Kakaï, Romain; Seifert, Thomas

    2016-10-01

    The relationship between biodiversity and ecosystem function has increasingly been debated as the cornerstone of the processes behind ecosystem services delivery. Experimental and natural field-based studies have come up with nonconsistent patterns of biodiversity-ecosystem function, supporting either niche complementarity or selection effects hypothesis. Here, we used aboveground carbon (AGC) storage as proxy for ecosystem function in a South African mistbelt forest, and analyzed its relationship with species diversity, through functional diversity and functional dominance. We hypothesized that (1) diversity influences AGC through functional diversity and functional dominance effects; and (2) effects of diversity on AGC would be greater for functional dominance than for functional diversity. Community weight mean (CWM) of functional traits (wood density, specific leaf area, and maximum plant height) were calculated to assess functional dominance (selection effects). As for functional diversity (complementarity effects), multitrait functional diversity indices were computed. The first hypothesis was tested using structural equation modeling. For the second hypothesis, effects of environmental variables such as slope and altitude were tested first, and separate linear mixed-effects models were fitted afterward for functional diversity, functional dominance, and both. Results showed that AGC varied significantly along the slope gradient, with lower values at steeper sites. Species diversity (richness) had positive relationship with AGC, even when slope effects were considered. As predicted, diversity effects on AGC were mediated through functional diversity and functional dominance, suggesting that both the niche complementarity and the selection effects are not exclusively affecting carbon storage. However, the effects were greater for functional diversity than for functional dominance. Furthermore, functional dominance effects were strongly transmitted by CWM of

  15. Bacterial community structure and diversity responses to the direct revegetation of an artisanal zinc smelting slag after 5 years.

    Science.gov (United States)

    Luo, Youfa; Wu, Yonggui; Wang, Hu; Xing, Rongrong; Zheng, Zhilin; Qiu, Jing; Yang, Lian

    2018-05-01

    This comparative field study examined the responses of bacterial community structure and diversity to the revegetation of zinc (Zn) smelting waste slag with eight plant species after 5 years. The microbial community structure of waste slag with and without vegetation was evaluated using high-throughput sequencing. The physiochemical properties of Zn smelting slag after revegetation with eight plant rhizospheres for 5 years were improved compared to those of bulk slag. Revegetation significantly increased the microbial community diversity in plant rhizospheres, and at the phylum level, Proteobacteria, Acidobacteria, and Bacteroidetes were notably more abundant in rhizosphere slags than those in bulk waste slag. Additionally, revegetation increased the relative abundance of plant growth-promoting rhizobacteria such as Flavobacterium, Streptomyces, and Arthrobacter as well as symbiotic N 2 fixers such as Bradyrhizobium. Three dominant native plant species (Arundo donax, Broussonetia papyrifera, and Robinia pseudoacacia) greatly increased the quality of the rhizosphere slags. Canonical correspondence analysis showed that the differences in bacterial community structure between the bulk and rhizosphere slags were explained by slag properties, i.e., pH, available copper (Cu) and lead (Pb), moisture, available nitrogen (N), phosphorus (P), and potassium (K), and organic matter (OM); however, available Zn and cadmium (Cd) contents were the slag parameters that best explained the differences between the rhizosphere communities of the eight plant species. The results suggested that revegetation plays an important role in enhancing bacterial community abundance and diversity in rhizosphere slags and that revegetation may also regulate microbiological properties and diversity mainly through changes in heavy metal bioavailability and physiochemical slag characteristics.

  16. Bacterial diversity in faeces from polar bear (Ursus maritimus in Arctic Svalbard

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    Brusetti Lorenzo

    2010-01-01

    Full Text Available Abstract Background Polar bears (Ursus maritimus are major predators in the Arctic marine ecosystem, feeding mainly on seals, and living closely associated with sea ice. Little is known of their gut microbial ecology and the main purpose of this study was to investigate the microbial diversity in faeces of polar bears in Svalbard, Norway (74-81°N, 10-33°E. In addition the level of blaTEM alleles, encoding ampicillin resistance (ampr were determined. In total, ten samples were collected from ten individual bears, rectum swabs from five individuals in 2004 and faeces samples from five individuals in 2006. Results A 16S rRNA gene clone library was constructed, and all sequences obtained from 161 clones showed affiliation with the phylum Firmicutes, with 160 sequences identified as Clostridiales and one sequence identified as unclassified Firmicutes. The majority of the sequences (70% were affiliated with the genus Clostridium. Aerobic heterotrophic cell counts on chocolate agar ranged between 5.0 × 104 to 1.6 × 106 colony forming units (cfu/ml for the rectum swabs and 4.0 × 103 to 1.0 × 105 cfu/g for the faeces samples. The proportion of ampr bacteria ranged from 0% to 44%. All of 144 randomly selected ampr isolates tested positive for enzymatic β-lactamase activity. Three % of the ampr isolates from the rectal samples yielded positive results when screened for the presence of blaTEM genes by PCR. BlaTEM alleles were also detected by PCR in two out of three total faecal DNA samples from polar bears. Conclusion The bacterial diversity in faeces from polar bears in their natural environment in Svalbard is low compared to other animal species, with all obtained clones affiliating to Firmicutes. Furthermore, only low levels of blaTEM alleles were detected in contrast to their increasing prevalence in some clinical and commensal bacterial populations.

  17. Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard.

    Science.gov (United States)

    Glad, Trine; Bernhardsen, Pål; Nielsen, Kaare M; Brusetti, Lorenzo; Andersen, Magnus; Aars, Jon; Sundset, Monica A

    2010-01-14

    Polar bears (Ursus maritimus) are major predators in the Arctic marine ecosystem, feeding mainly on seals, and living closely associated with sea ice. Little is known of their gut microbial ecology and the main purpose of this study was to investigate the microbial diversity in faeces of polar bears in Svalbard, Norway (74-81 degrees N, 10-33 degrees E). In addition the level of blaTEM alleles, encoding ampicillin resistance (ampr) were determined. In total, ten samples were collected from ten individual bears, rectum swabs from five individuals in 2004 and faeces samples from five individuals in 2006. A 16S rRNA gene clone library was constructed, and all sequences obtained from 161 clones showed affiliation with the phylum Firmicutes, with 160 sequences identified as Clostridiales and one sequence identified as unclassified Firmicutes. The majority of the sequences (70%) were affiliated with the genus Clostridium. Aerobic heterotrophic cell counts on chocolate agar ranged between 5.0 x 10(4) to 1.6 x 10(6) colony forming units (cfu)/ml for the rectum swabs and 4.0 x 10(3) to 1.0 x 10(5) cfu/g for the faeces samples. The proportion of ampr bacteria ranged from 0% to 44%. All of 144 randomly selected ampr isolates tested positive for enzymatic beta-lactamase activity. Three % of the ampr isolates from the rectal samples yielded positive results when screened for the presence of blaTEM genes by PCR. BlaTEM alleles were also detected by PCR in two out of three total faecal DNA samples from polar bears. The bacterial diversity in faeces from polar bears in their natural environment in Svalbard is low compared to other animal species, with all obtained clones affiliating to Firmicutes. Furthermore, only low levels of blaTEM alleles were detected in contrast to their increasing prevalence in some clinical and commensal bacterial populations.

  18. Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard

    Science.gov (United States)

    2010-01-01

    Background Polar bears (Ursus maritimus) are major predators in the Arctic marine ecosystem, feeding mainly on seals, and living closely associated with sea ice. Little is known of their gut microbial ecology and the main purpose of this study was to investigate the microbial diversity in faeces of polar bears in Svalbard, Norway (74-81°N, 10-33°E). In addition the level of blaTEM alleles, encoding ampicillin resistance (ampr) were determined. In total, ten samples were collected from ten individual bears, rectum swabs from five individuals in 2004 and faeces samples from five individuals in 2006. Results A 16S rRNA gene clone library was constructed, and all sequences obtained from 161 clones showed affiliation with the phylum Firmicutes, with 160 sequences identified as Clostridiales and one sequence identified as unclassified Firmicutes. The majority of the sequences (70%) were affiliated with the genus Clostridium. Aerobic heterotrophic cell counts on chocolate agar ranged between 5.0 × 104 to 1.6 × 106 colony forming units (cfu)/ml for the rectum swabs and 4.0 × 103 to 1.0 × 105 cfu/g for the faeces samples. The proportion of ampr bacteria ranged from 0% to 44%. All of 144 randomly selected ampr isolates tested positive for enzymatic β-lactamase activity. Three % of the ampr isolates from the rectal samples yielded positive results when screened for the presence of blaTEM genes by PCR. BlaTEM alleles were also detected by PCR in two out of three total faecal DNA samples from polar bears. Conclusion The bacterial diversity in faeces from polar bears in their natural environment in Svalbard is low compared to other animal species, with all obtained clones affiliating to Firmicutes. Furthermore, only low levels of blaTEM alleles were detected in contrast to their increasing prevalence in some clinical and commensal bacterial populations. PMID:20074323

  19. Bacterial cellulose biosynthesis: diversity of operons, subunits, products and functions

    Science.gov (United States)

    Römling, Ute; Galperin, Michael Y.

    2015-01-01

    Summary Recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. In most studied bacteria, just two subunits, BcsA and BcsB, are necessary and sufficient for the formation of the polysaccharide chain in vitro. Other subunits – which differ among various taxa – affect the enzymatic activity and product yield in vivo by modulating expression of biosynthesis apparatus, export of the nascent β-D-glucan polymer to the cell surface, and the organization of cellulose fibers into a higher-order structure. These auxiliary subunits play key roles in determining the quantity and structure of the resulting biofilm, which is particularly important for interactions of bacteria with higher organisms that lead to rhizosphere colonization and modulate virulence of cellulose-producing bacterial pathogens inside and outside of host cells. Here we review the organization of four principal types of cellulose synthase operons found in various bacterial genomes, identify additional bcs genes that encode likely components of the cellulose biosynthesis and secretion machinery, and propose a unified nomenclature for these genes and subunits. We also discuss the role of cellulose as a key component of biofilms formed by a variety of free-living and pathogenic bacteria and, for the latter, in the choice between acute infection and persistence in the host. PMID:26077867

  20. Biogeographical distribution and diversity of bacterial communities in surface sediments of the South China Sea.

    Science.gov (United States)

    Li, Tao; Wang, Peng

    2013-05-01

    This paper aims at an investigation of the features of bacterial communities in surface sediments of the South China Sea (SCS). In particular, biogeographical distribution patterns and the phylogenetic diversity of bacteria found in sediments collected from a coral reef platform, a continental slope, and a deep-sea basin were determined. Bacterial diversity was measured by an observation of 16S rRNA genes, and 18 phylogenetic groups were identified in the bacterial clone library. Planctomycetes, Deltaproteobacteria, candidate division OP11, and Alphaproteobacteria made up the majority of the bacteria in the samples, with their mean bacterial clones being 16%, 15%, 12%, and 9%, respectively. By comparison, the bacterial communities found in the SCS surface sediments were significantly different from other previously observed deep-sea bacterial communities. This research also emphasizes the fact that geographical factors have an impact on the biogeographical distribution patterns of bacterial communities. For instance, canonical correspondence analyses illustrated that the percentage of sand weight and water depth are important factors affecting the bacterial community composition. Therefore, this study highlights the importance of adequately determining the relationship between geographical factors and the distribution of bacteria in the world's seas and oceans.

  1. [Bacterial diversity within different sections of summer sea-ice samples from the Prydz Bay, Antarctica].

    Science.gov (United States)

    Ma, Jifei; Du, Zongjun; Luo, Wei; Yu, Yong; Zeng, Yixin; Chen, Bo; Li, Huirong

    2013-02-04

    In order to assess bacterial abundance and diversity within three different sections of summer sea-ice samples collected from the Prydz Bay, Antarctica. Fluorescence in situ hybridization was applied to determine the proportions of Bacteria in sea-ice. Bacterial community composition within sea ice was analyzed by 16S rRNA gene clone library construction. Correlation analysis was performed between the physicochemical parameters and the bacterial diversity and abundance within sea ice. The result of fluorescence in situ hybridization shows that bacteria were abundant in the bottom section, and the concentration of total organic carbon, total organic nitrogen and phosphate may be the main factors for bacterial abundance. In bacterial 16S rRNA gene libraries of sea-ice, nearly complete 16S rRNA gene sequences were grouped into three distinct lineages of Bacteria (gamma-Proteobacteria, alpha-Proteobacteria and Bacteroidetes). Most clone sequences were related to cultured bacterial isolates from the marine environment, arctic and Antarctic sea-ice with high similarity. The member of Bacteroidetes was not detected in the bottom section of sea-ice. The bacterial communities within sea-ice were little heterogeneous at the genus-level between different sections, and the concentration of NH4+ may cause this distribution. The number of bacteria was abundant in the bottom section of sea-ice. Gamma-proteobacteria was the dominant bacterial lineage in sea-ice.

  2. Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area

    Directory of Open Access Journals (Sweden)

    Nabanita Mukherjee

    2014-12-01

    Full Text Available Public fitness centers and exercise facilities have been implicated as possible sources for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial community residing on the surfaces in these indoor environments is still unknown. In this study, we investigated the overall bacterial ecology of selected fitness centers in a metropolitan area (Memphis, TN, USA utilizing culture-independent pyrosequencing of the 16S rRNA genes. Samples were collected from the skin-contact surfaces (e.g., exercise instruments, floor mats, handrails, etc. within fitness centers. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Proteobacter and Actinobacteria, with a total of 17 bacterial families and 25 bacterial genera. Most of these bacterial genera are of human and environmental origin (including, air, dust, soil, and water. Additionally, we found the presence of some pathogenic or potential pathogenic bacterial genera including Salmonella, Staphylococcus, Klebsiella, and Micrococcus. Staphylococcus was found to be the most prevalent genus. Presence of viable forms of these pathogens elevates risk of exposure of any susceptible individuals. Several factors (including personal hygiene, surface cleaning and disinfection schedules of the facilities may be the reasons for the rich bacterial diversity found in this study. The current finding underscores the need to increase public awareness on the importance of personal hygiene and sanitation for public gym users.

  3. Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen.

    Science.gov (United States)

    Do, Thi Huyen; Dao, Trong Khoa; Nguyen, Khanh Hoang Viet; Le, Ngoc Giang; Nguyen, Thi Mai Phuong; Le, Tung Lam; Phung, Thu Nguyet; van Straalen, Nico M; Roelofs, Dick; Truong, Nam Hai

    2018-05-01

    In a previous study, analysis of Illumina sequenced metagenomic DNA data of bacteria in Vietnamese goats' rumen showed a high diversity of putative lignocellulolytic genes. In this study, taxonomy speculation of microbial community and lignocellulolytic bacteria population in the rumen was conducted to elucidate a role of bacterial structure for effective degradation of plant materials. The metagenomic data had been subjected into Basic Local Alignment Search Tool (BLASTX) algorithm and the National Center for Biotechnology Information non-redundant sequence database. Here the BLASTX hits were further processed by the Metagenome Analyzer program to statistically analyze the abundance of taxa. Microbial community in the rumen is defined by dominance of Bacteroidetes compared to Firmicutes. The ratio of Firmicutes versus Bacteroidetes was 0.36:1. An abundance of Synergistetes was uniquely identified in the goat microbiome may be formed by host genotype. With regard to bacterial lignocellulose degraders, the ratio of lignocellulolytic genes affiliated with Firmicutes compared to the genes linked to Bacteroidetes was 0.11:1, in which the genes encoding putative hemicellulases, carbohydrate esterases, polysaccharide lyases originated from Bacteroidetes were 14 to 20 times higher than from Firmicutes. Firmicutes seem to possess more cellulose hydrolysis capacity showing a Firmicutes/Bacteroidetes ratio of 0.35:1. Analysis of lignocellulolytic potential degraders shows that four species belonged to Bacteroidetes phylum, while two species belonged to Firmicutes phylum harbouring at least 12 different catalytic domains for all lignocellulose pretreatment, cellulose, as well as hemicellulose saccharification. Based on these findings, we speculate that increasing the members of Bacteroidetes to keep a low ratio of Firmicutes versus Bacteroidetes in goat rumen has resulted most likely in an increased lignocellulose digestion.

  4. Bacterial diversity associated with Cinachyra cavernosa and Haliclona pigmentifera, cohabiting sponges in the coral reef ecosystem of Gulf of Mannar, southeast coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Jasmin, C; Anas, A.; Nair, S.

    1.97). UniFrac analysis confirmed the difference in bacterial diversity of the two sponge species and also between the sponges and the reef water(p<0.001). The results of our study restate the existence of a host driven force in shaping the sponge...

  5. Diversity and distribution of entomopathogenic nematodes (Nematoda: Steinernematidae, Heterorhabditidae) and their bacterial symbionts (gamma-Proteobacteria: Enterobacteriaceae) in Jordan.

    Science.gov (United States)

    Stock, S Patricia; Al Banna, Luma; Darwish, Rula; Katbeh, Ahmad

    2008-06-01

    Until now, only a few systematic surveys of entomopathogenic nematodes (EPN) have been conducted in Middle Eastern countries. Many of the recovered EPN species in this region have shown to own distinctive qualities that enable their survival in unique environments, such as high temperatures and low moisture levels tolerance. These new species and strains, with unique environmental tolerances, are more suitable for their consideration in pest management programs in xerophytic regions. With this background in mind, we recently conducted a survey of EPN in Jordan. This study records for the first time the diversity and distribution of these nematodes and their bacterial symbionts in this country. Jordan's three geographic regions: (1) the highlands, (2) Jordan valley and (3) the desert region were sampled. Within each region, natural habitats and agricultural regions characteristic to each region were considered for sampling purposes. Four EPN species including three Steinernema and one Heterorhabditis were recovered. Nematodes were identified using a combination of molecular markers and classic morphological diagnostic tools. Bacterial symbionts were identified by analysis of 16S rRNA sequences. Abiotic characteristics such as soil type, soil pH, and elevation were also recorded. We herein report the diversity of EPN species in Jordan and discuss their potential in Biocontrol and IPM programs for this country.

  6. Ecological mechanisms underlying arthropod species diversity in grasslands.

    Science.gov (United States)

    Joern, Anthony; Laws, Angela N

    2013-01-01

    Arthropods are an important component of grassland systems, contributing significantly to biodiversity and ecosystem structure and function. Climate, fire, and grazing by large herbivores are important drivers in grasslands worldwide. Arthropod responses to these drivers are highly variable and clear patterns are difficult to find, but responses are largely indirect with respect to changes in resources, species interactions, habitat structure, and habitat heterogeneity resulting from interactions among fire, grazing, and climate. Here, we review these ecological mechanisms influencing grassland arthropod diversity. We summarize hypotheses describing species diversity at local and regional scales and then discuss specific factors that may affect arthropod diversity in grassland systems. These factors include direct and indirect effects of grazing, fire, and climate, species interactions, above- and belowground interactions, and landscape-level effects.

  7. Bacterial community diversity in a low-permeability oil reservoir and its potential for enhancing oil recovery.

    Science.gov (United States)

    Xiao, Meng; Zhang, Zhong-Zhi; Wang, Jing-Xiu; Zhang, Guang-Qing; Luo, Yi-Jing; Song, Zhao-Zheng; Zhang, Ji-Yuan

    2013-11-01

    The diversity of indigenous bacterial community and the functional species in the water samples from three production wells of a low permeability oil reservoir was investigated by high-throughput sequencing technology. The potential of application of indigenous bacteria for enhancing oil recovery was evaluated by examination of the effect of bacterial stimulation on the formation water-oil-rock surface interactions and micromodel test. The results showed that production well 88-122 had the most diverse bacterial community and functional species. The broth of indigenous bacteria stimulated by an organic nutrient activator at aerobic condition changed the wettability of the rock surface from oil-wet to water-wet. Micromodel test results showed that flooding using stimulated indigenous bacteria following water flooding improved oil recovery by 6.9% and 7.7% in fractured and unfractured micromodels, respectively. Therefore, the zone of low permeability reservoir has a great potential for indigenous microbial enhanced oil recovery. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Identification and diversity of Fusarium species isolated from tomato fruits

    Directory of Open Access Journals (Sweden)

    Murad Nur Baiti Abd

    2016-07-01

    Full Text Available Fruit rot of tomato is a serious disease caused by Fusarium species. Sampling was conducted throughout Selangor, Malaysia and fungal species identification was conducted based on morphological and gene encoding translation elongation factor 1-α (tef1-α sequence analysis. Five species of Fusarium were discovered namely F. oxysporum (including F. oxysporum f. sp. lycopersici, F. solani, F. equiseti, F. proliferatum and F. verticillioides. Our results provide additional information regarding the diversity of Fusarium species associated with fruit rot disease of tomato.

  9. Comparative analysis of the intestinal bacterial communities in different species of carp by pyrosequencing.

    Science.gov (United States)

    Li, Tongtong; Long, Meng; Gatesoupe, François-Joël; Zhang, Qianqian; Li, Aihua; Gong, Xiaoning

    2015-01-01

    Gut microbiota is increasingly regarded as an integral component of the host, due to important roles in the modulation of the immune system, the proliferation of the intestinal epithelium and the regulation of the dietary energy intake. Understanding the factors that influence the composition of these microbial communities is essential to health management, and the application to aquatic animals still requires basic investigation. In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. The specimens of the three species were cohabiting in the same pond. Between 6,218 and 10,220 effective sequences were read from each sample, resulting in a total of 110,398 sequences for 13 samples from gut microbiota and pond water. In general, the microbial communities of the three carps were dominated by Fusobacteria, Firmicutes, Proteobacteria and Bacteroidetes, but the abundance of each phylum was significantly different between species. At the genus level, the overwhelming group was Cetobacterium (97.29 ± 0.46 %) in crucian carp, while its abundance averaged c. 40 and 60 % of the sequences read in the other two species. There was higher microbial diversity in the gut of filter-feeding bighead carp than the gut of the two other species, with grazing feeding habits. The composition of intestine microbiota of grass carp and crucian carp shared higher similarity when compared with bighead carp. The principal coordinates analysis (PCoA) with the weighted UniFrac distance and the heatmap analysis suggested that gut microbiota was not a simple reflection of the microbial community in the local habitat but resulted from species-specific selective pressures, possibly dependent on behavioural, immune

  10. Birds' species diversity measurement of Uchali Wetland (Ramsar site Pakistan

    Directory of Open Access Journals (Sweden)

    Taofik Oyedele Dauda

    2017-06-01

    Full Text Available We carried out this study to evaluate bird species diversity and to model bird species abundance using Uchali Wetland, Pakistan (32°33′N, 72°01′E. Data obtained were subjected to summary statistics, Simpson diversity, Shannon evenness index, and rank abundance curve and model. The watershed supports 25,361 birds of 47 species, which is appreciably less than the number of bird species supported by the same wetland in the past year (1991. Total evenness could be obtained as the ranks increases and this differed annually. Evenness index (EI analysis showed that EI for 2011 was 0.0231, for 2012, it was 0.02, for 2013, it was 0.01, and for the annual mean, it was 0.046 indicating functional abundance of the species. Bird species diversity measurement could be enhanced by the use of the modified rank–abundance curve and would clearly present the true picture of the bird species abundance.

  11. Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile.

    Science.gov (United States)

    Zhu, Renbin; Shi, Yu; Ma, Dawei; Wang, Can; Xu, Hua; Chu, Haiyan

    2015-11-25

    Current penguin activity in Antarctica affects the geochemistry of sediments and their microbial communities; the effects of historical penguin activity are less well understood. Here, bacterial diversity in ornithogenic sediment was investigated using high-throughput pyrosequencing. The relative abundances of dominant phyla were controlled by the amount of historical penguin guano deposition. Significant positive correlations were found between both the bacterial richness and diversity, and the relative penguin number (p penguin activity drove the vertical distribution of the bacterial communities. The lowest relative abundances of individual phyla corresponded to lowest number of penguin population at 1,800-2,300 yr BP during a drier and colder period; the opposite was observed during a moister and warmer climate (1,400-1,800 yr BP). This study shows that changes in the climate over millennia affected penguin populations and the outcomes of these changes affect the sediment bacterial community today.

  12. Novel acsF Gene Primers Revealed a Diverse Phototrophic Bacterial Population, Including Gemmatimonadetes, in Lake Taihu (China)

    DEFF Research Database (Denmark)

    Huang, Yili; Zeng, Yanhua; Lu, Hang

    2016-01-01

    Seq sequencing of the 16S rRNA, pufM, and bchY genes was carried out to assess the diversity of local phototrophic communities. In addition, we designed new degenerate primers of aerobic cyclase gene acsF, which serves as a convenient marker for both phototrophic Gemmatimonadetes and phototrophic Proteobacteria...... a diverse community of phototrophic Gemmatimonadetes forming 30 operational taxonomic units. These species represented 10.5 and 17.3% of the acsF reads in the upper semiaerobic sediment and anoxic sediment, whereas their abundance in the water column was ... fundamental biological processes on Earth. Recently, the presence of photosynthetic reaction centers has been reported from a rarely studied bacterial phylum, Gemmatimonadetes, but almost nothing is known about the diversity and environmental distribution of these organisms. The newly designed acsF primers...

  13. Comparative approach to capture bacterial diversity in coastal waters

    DEFF Research Database (Denmark)

    Na, Hyunsoo; Kim, Ok-Sun; Yoon, Suk-hwan

    2011-01-01

    Despite the revolutionary advancements in DNA sequencing technology and cultivation techniques, few studies have been done to directly compare these methods. In this study, a 16S rRNA gene-based, integrative approach combining culture-independent techniques with culture-dependent methods was taken...... to investigate the bacterial community structure of coastal seawater collected from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions from the water...

  14. Weed species diversity in organic and integrated farming systems

    Directory of Open Access Journals (Sweden)

    Magdalena Jastrzębska

    2013-10-01

    Full Text Available Phytosociological data were collected in 1994–1996 in plots (relevés at the Research Station for Organic Farming and Conservation Breeding of the Polish Academy of Sciences in Popielno included in a large-area experiment conducted according to the concept and method proposed by Prof. S. Nawrocki. In a four-field crop rotation (root crops – spring barley undersown with red clover and grasses – red clover/grass mixture – winter triticale, each field was divided into two management units, organic and integrated. Data were collected in relevés by the Braun-Blanquet method, each year at the peak of the growing season. Weed abundance (% cover in cultivated fields and the number of weed species (species richness in crops were determined, which provided a basis for calculating the Shannon-Wiener indices of species diversity and evenness, and the Rényi profiles. The qualitative (species and quantitative structure of weed communities was compared using the Sørensen index. A total of 115 weed taxa (species, subspecies and varieties were identified in the examined agro-phytocenoses. Echinochloa crus-galli, Chenopodium album, Matricaria maritima subsp. inodora, Capsella bursa-pastoris, Thlaspi arvense and Stellaria media were the most abundant. Weed infestation was slightly higher in the organic farming system than in the integrated system. Organic farming contributed to higher weed species diversity in root crops, red clover/grass mixtures and winter triticale. Weed species richness was reduced in red clover/grass stands, while root crops and – to a lesser degree – spring barley undersown with red clover and grasses decreased weed species diversity. The species composition and in particular the quantitative structure of weeds were affected by crop species and cultivation regime rather than by the farming system. Weed communities of crops grown under organic and integrated farming systems were more similar with regard to species composition

  15. Cultivable bacterial diversity along the altitudinal zonation and vegetation range of tropical Eastern Himalaya

    Directory of Open Access Journals (Sweden)

    Nathaniel A. Lyngwi

    2013-03-01

    Full Text Available The Northeastern part of India sprawls over an area of 262 379km² in the Eastern Himalayan range. This constitutes a biodiversity hotspot with high levels of biodiversity and endemism; unfortunately, is also a poorly known area, especially on its microbial diversity. In this study, we assessed cultivable soil bacterial diversity and distribution from lowlands to highlands (34 to 3 990m.a.s.l.. Soil physico-chemical parameters and forest types across the different altitudes were characterized and correlated with bacterial distribution and diversity. Microbes from the soil samples were grown in Nutrient, Muller Hinton and Luria-Bertani agar plates and were initially characterized using biochemical methods. Parameters like dehydrogenase and urease activities, temperature, moisture content, pH, carbon content, bulk density of the sampled soil were measured for each site. Representative isolates were also subjected to 16S rDNA sequence analysis. A total of 155 cultivable bacterial isolates were characterized which were analyzed for richness, evenness and diversity indices. The tropical and sub-tropical forests supported higher bacterial diversity compared to temperate pine, temperate conifer, and sub-alpine rhododendron forests. The 16S rRNA phylogenetic analysis revealed that Firmicutes was the most common group followed by Proteobacteria and Bacteroidetes. Species belonging to the genera Bacillus and Pseudomonas were the most abundant. Bacterial CFU showed positive but insignificant correlation with soil parameters like pH (r=0.208, soil temperature (r=0.303, ambient temperature (r=0.443, soil carbon content (r=0.525, soil bulk density (r=0.268, soil urease (r=0.549 and soil dehydrogenase (r=0.492. Altitude (r=0.561 and soil moisture content (r=-0.051 showed negative correlation. Altitudinal gradient along with the vegetation and soil physico-chemical parameters were found to influence bacterial diversity and distribution. This study points out

  16. Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits

    Directory of Open Access Journals (Sweden)

    Ara S. Winter

    2017-10-01

    Full Text Available Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS, in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.

  17. Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits.

    Science.gov (United States)

    Winter, Ara S; Hathaway, Jennifer J M; Kimble, Jason C; Buecher, Debbie C; Valdez, Ernest W; Porras-Alfaro, Andrea; Young, Jesse M; Read, Kaitlyn J H; Northup, Diana E

    2017-01-01

    Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host's health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.

  18. Broad spectrum microarray for fingerprint-based bacterial species identification

    Directory of Open Access Journals (Sweden)

    Frey Jürg E

    2010-02-01

    Full Text Available Abstract Background Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays are limited to organisms for which specific probes are available, and often have difficulty discriminating closely related taxa. We have developed an alternative broad-spectrum microarray that employs hybridisation fingerprints generated by high-density anonymous markers distributed over the entire genome for identification based on comparison to a reference database. Results A high-density microarray carrying 95,000 unique 13-mer probes was designed. Optimized methods were developed to deliver reproducible hybridisation patterns that enabled confident discrimination of bacteria at the species, subspecies, and strain levels. High correlation coefficients were achieved between replicates. A sub-selection of 12,071 probes, determined by ANOVA and class prediction analysis, enabled the discrimination of all samples in our panel. Mismatch probe hybridisation was observed but was found to have no effect on the discriminatory capacity of our system. Conclusions These results indicate the potential of our genome chip for reliable identification of a wide range of bacterial taxa at the subspecies level without laborious prior sequencing and probe design. With its high resolution capacity, our proof-of-principle chip demonstrates great potential as a tool for molecular diagnostics of broad taxonomic groups.

  19. PCR-DGGE assessment of the bacterial diversity of breast milk in women with lactational infectious mastitis.

    Science.gov (United States)

    Delgado, Susana; Arroyo, Rebeca; Martín, Rocío; Rodríguez, Juan M

    2008-04-18

    Infectious mastitis is a common condition during lactation and in fact, represents one of the main causes leading to a precocious weaning. The number of studies dealing with lactational mastitis is low and, up to now, the etiological diagnosis is frequently made on the basis of unspecific clinical signs. The aim of this study was to investigate the microbial diversity of breast milk in 20 women with lactational mastitis employing culture-dependent and culture-independent (PCR-DGGE) approaches. Breast milk samples were cultured in different media to investigate the presence of bacteria and/or yeasts, and a total of 149 representative isolates were identified to the species level by 16S rRNA gene PCR sequencing. The microorganisms recovered were compared with those found by PCR-DGGE analysis. To identify the DGGE profiles two reference markers of different microbial species were constructed. Sequence analysis of unknown bands was also performed. Staphylococci were the dominant bacterial group and Staphylococcus epidermidis was the dominant species. In a lower number of samples, other bacteria (mainly streptococci and a few gram-negative species) were also identified. Globally, PCR-DGGE results showed a good correlation with those obtained by culture-based methods. However, although DNA bands corresponding to different lactic acid bacteria were detected, such bacteria could not be isolated from the milk samples. Staphylococci seem to be the main etiological agents of human lactational mastitis. The combined use of culture and molecular techniques allowed a better characterization of the bacterial diversity in milk from women suffering from infectious mastitis. Our results suggest that this condition could be the result of a disbiotic process where some of the bacterial species usually present in human milk outgrow (staphylococci) while others disappear (lactobacilli or lactococci).

  20. Bacterial diversity of biofilm samples from deep mines in South ...

    African Journals Online (AJOL)

    JTEkanem

    Department of Biotechnology, University of The Free State, Box 339, ... Proteobacteria, forty-one percent (41%) of the sequences with yet uncultured bacteria and ..... (1995) Selective solid media for isolating and enumerating acidophilic bacteria. ... Monitoring the Lactic Acid Bacteria diversity during Shochu fermentation by.

  1. Measuring β-diversity with species abundance data.

    Science.gov (United States)

    Barwell, Louise J; Isaac, Nick J B; Kunin, William E

    2015-07-01

    In 2003, 24 presence-absence β-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of β-diversity. β-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. We test 16 conceptual properties and two sampling properties of a β-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of β than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (βA,B  = βB,A ), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer β-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence-absence metric, βsim , performed well overall. Only

  2. Temporal and Spatial Diversity of Bacterial Communities in Coastal Waters of the South China Sea

    Science.gov (United States)

    Du, Jikun; Xiao, Kai; Li, Li; Ding, Xian; Liu, Helu; Lu, Yongjun; Zhou, Shining

    2013-01-01

    Bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems. Temporal and geographical patterns in ocean bacterial communities have been observed in many studies, but the temporal and spatial patterns in the bacterial communities from the South China Sea remained unexplored. To determine the spatiotemporal patterns, we generated 16S rRNA datasets for 15 samples collected from the five regularly distributed sites of the South China Sea in three seasons (spring, summer, winter). A total of 491 representative sequences were analyzed by MOTHUR, yielding 282 operational taxonomic units (OTUs) grouped at 97% stringency. Significant temporal variations of bacterial diversity were observed. Richness and diversity indices indicated that summer samples were the most diverse. The main bacterial group in spring and summer samples was Alphaproteobacteria, followed by Cyanobacteria and Gammaproteobacteria, whereas Cyanobacteria dominated the winter samples. Spatial patterns in the samples were observed that samples collected from the coastal (D151, D221) waters and offshore (D157, D1512, D224) waters clustered separately, the coastal samples harbored more diverse bacterial communities. However, the temporal pattern of the coastal site D151 was contrary to that of the coastal site D221. The LIBSHUFF statistics revealed noticeable differences among the spring, summer and winter libraries collected at five sites. The UPGMA tree showed there were temporal and spatial heterogeneity of bacterial community composition in coastal waters of the South China Sea. The water salinity (P=0.001) contributed significantly to the bacteria-environment relationship. Our results revealed that bacterial community structures were influenced by environmental factors and community-level changes in 16S-based diversity were better explained by spatial patterns than by temporal patterns. PMID:23785512

  3. Resource diversity and provenance underpin spatial patterns in functional diversity across native and exotic species.

    Science.gov (United States)

    Méndez, Verónica; Wood, Jamie R; Butler, Simon J

    2018-05-01

    Functional diversity metrics are increasingly used to augment or replace taxonomic diversity metrics to deliver more mechanistic insights into community structure and function. Metrics used to describe landscape structure and characteristics share many of the same limitations as taxonomy-based metrics, particularly their reliance on anthropogenically defined typologies with little consideration of structure, management, or function. However, the development of alternative metrics to describe landscape characteristics has been limited. Here, we extend the functional diversity framework to characterize landscapes based on the diversity of resources available across habitats present. We then examine the influence of resource diversity and provenance on the functional diversities of native and exotic avian communities in New Zealand. Invasive species are increasingly prevalent and considered a global threat to ecosystem function, but the characteristics of and interactions between sympatric native and exotic communities remain unresolved. Understanding their comparative responses to environmental change and the mechanisms underpinning them is of growing importance in predicting community dynamics and changing ecosystem function. We use (i) matrices of resource use (species) and resource availability (habitats) and (ii) occurrence data for 62 native and 25 exotic species and 19 native and 13 exotic habitats in 2015 10 × 10 km quadrats to examine the relationship between native and exotic avian and landscape functional diversity. The numbers of species in, and functional diversities of, native and exotic communities were positively related. Each community displayed evidence of environmental filtering, but it was significantly stronger for exotic species. Less environmental filtering occurred in landscapes providing a more diverse combination of resources, with resource provenance also an influential factor. Landscape functional diversity explained a greater

  4. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    KAUST Repository

    Lee, Onon

    2010-11-18

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. © 2011 International Society for Microbial Ecology All rights reserved.

  5. A Meta-Analysis of the Bacterial and Archaeal Diversity Observed in Wetland Soils

    Directory of Open Access Journals (Sweden)

    Xiaofei Lv

    2014-01-01

    Full Text Available This study examined the bacterial and archaeal diversity from a worldwide range of wetlands soils and sediments using a meta-analysis approach. All available 16S rRNA gene sequences recovered from wetlands in public databases were retrieved. In November 2012, a total of 12677 bacterial and 1747 archaeal sequences were collected in GenBank. All the bacterial sequences were assigned into 6383 operational taxonomic units (OTUs 0.03, representing 31 known bacterial phyla, predominant with Proteobacteria (2791 OTUs, Bacteroidetes (868 OTUs, Acidobacteria (731 OTUs, Firmicutes (540 OTUs, and Actinobacteria (418 OTUs. The genus Flavobacterium (11.6% of bacterial sequences was the dominate bacteria in wetlands, followed by Gp1, Nitrosospira, and Nitrosomonas. Archaeal sequences were assigned to 521 OTUs from phyla Euryarchaeota and Crenarchaeota. The dominating archaeal genera were Fervidicoccus and Methanosaeta. Rarefaction analysis indicated that approximately 40% of bacterial and 83% of archaeal diversity in wetland soils and sediments have been presented. Our results should be significant for well-understanding the microbial diversity involved in worldwide wetlands.

  6. Genetic calibration of species diversity among North America's freshwater fishes

    OpenAIRE

    April, Julien; Mayden, Richard L.; Hanner, Robert H.; Bernatchez, Louis

    2011-01-01

    Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a mor...

  7. Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment.

    Directory of Open Access Journals (Sweden)

    Fabian Staubach

    Full Text Available The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila-associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.

  8. Characteristics of phylogenetic diversity in airborne bacterial populations in China

    Science.gov (United States)

    Chaudhry, Zahra; Santarpia, Joshua L.; Martins, J. V.

    2011-05-01

    Considering their potential implications for human health, agricultural productivity, and ecosystem stability, surprisingly little is known about the composition or dynamics of the atmosphere's biological aerosols. The few studies that have examined phylogenetic diversity in China focused on a single sampling period, whereas this study spans 3 months and includes over 300 samples. The 300+ samples were categorized by month and direction of their back-trajectory. DNA extraction was carried out on the pooled samples in a quantitative manner to allow for comparison between the amount of extracted material and the amount of initial total aerosol mass. Within an individual month, samples originating from similar land types and approximately equidistant to the sampling location exhibited similar diversity, whereas samples originating from much greater distances and from different land types included phyla unique to that location. Phyla from the same origin also varied from one month to the next. The biological diversity found from the Phylochips reinforces the hypothesis that air samples carry a biological record of their history.

  9. In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the red sea coral Acropora hemprichii.

    Science.gov (United States)

    Jessen, Christian; Villa Lizcano, Javier Felipe; Bayer, Till; Roder, Cornelia; Aranda, Manuel; Wild, Christian; Voolstra, Christian R

    2013-01-01

    Coral reefs of the Central Red Sea display a high degree of endemism, and are increasingly threatened by anthropogenic effects due to intense local coastal development measures. Overfishing and eutrophication are among the most significant local pressures on these reefs, but there is no information available about their potential effects on the associated microbial community. Therefore, we compared holobiont physiology and 16S-based bacterial communities of tissue and mucus of the hard coral Acropora hemprichii after 1 and 16 weeks of in-situ inorganic nutrient enrichment (via fertilizer diffusion) and/or herbivore exclusion (via caging) in an offshore reef of the Central Red Sea. Simulated eutrophication and/or overfishing treatments did not affect coral physiology with respect to coral respiration rates, chlorophyll a content, zooxanthellae abundance, or δ (15)N isotopic signatures. The bacterial community of A. hemprichii was rich and uneven, and diversity increased over time in all treatments. While distinct bacterial species were identified as a consequence of eutrophication, overfishing, or both, two bacterial species that could be classified to the genus Endozoicomonas were consistently abundant and constituted two thirds of bacteria in the coral. Several nitrogen-fixing and denitrifying bacteria were found in the coral specimens that were exposed to experimentally increased nutrients. However, no particular bacterial species was consistently associated with the coral under a given treatment and the single effects of manipulated eutrophication and overfishing could not predict the combined effect. Our data underlines the importance of conducting field studies in a holobiont framework, taking both, physiological and molecular measures into account.

  10. In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the red sea coral Acropora hemprichii.

    Directory of Open Access Journals (Sweden)

    Christian Jessen

    Full Text Available Coral reefs of the Central Red Sea display a high degree of endemism, and are increasingly threatened by anthropogenic effects due to intense local coastal development measures. Overfishing and eutrophication are among the most significant local pressures on these reefs, but there is no information available about their potential effects on the associated microbial community. Therefore, we compared holobiont physiology and 16S-based bacterial communities of tissue and mucus of the hard coral Acropora hemprichii after 1 and 16 weeks of in-situ inorganic nutrient enrichment (via fertilizer diffusion and/or herbivore exclusion (via caging in an offshore reef of the Central Red Sea. Simulated eutrophication and/or overfishing treatments did not affect coral physiology with respect to coral respiration rates, chlorophyll a content, zooxanthellae abundance, or δ (15N isotopic signatures. The bacterial community of A. hemprichii was rich and uneven, and diversity increased over time in all treatments. While distinct bacterial species were identified as a consequence of eutrophication, overfishing, or both, two bacterial species that could be classified to the genus Endozoicomonas were consistently abundant and constituted two thirds of bacteria in the coral. Several nitrogen-fixing and denitrifying bacteria were found in the coral specimens that were exposed to experimentally increased nutrients. However, no particular bacterial species was consistently associated with the coral under a given treatment and the single effects of manipulated eutrophication and overfishing could not predict the combined effect. Our data underlines the importance of conducting field studies in a holobiont framework, taking both, physiological and molecular measures into account.

  11. In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the red sea coral Acropora hemprichii.

    KAUST Repository

    Jessen, Christian

    2013-04-22

    Coral reefs of the Central Red Sea display a high degree of endemism, and are increasingly threatened by anthropogenic effects due to intense local coastal development measures. Overfishing and eutrophication are among the most significant local pressures on these reefs, but there is no information available about their potential effects on the associated microbial community. Therefore, we compared holobiont physiology and 16S-based bacterial communities of tissue and mucus of the hard coral Acropora hemprichii after 1 and 16 weeks of in-situ inorganic nutrient enrichment (via fertilizer diffusion) and/or herbivore exclusion (via caging) in an offshore reef of the Central Red Sea. Simulated eutrophication and/or overfishing treatments did not affect coral physiology with respect to coral respiration rates, chlorophyll a content, zooxanthellae abundance, or δ (15)N isotopic signatures. The bacterial community of A. hemprichii was rich and uneven, and diversity increased over time in all treatments. While distinct bacterial species were identified as a consequence of eutrophication, overfishing, or both, two bacterial species that could be classified to the genus Endozoicomonas were consistently abundant and constituted two thirds of bacteria in the coral. Several nitrogen-fixing and denitrifying bacteria were found in the coral specimens that were exposed to experimentally increased nutrients. However, no particular bacterial species was consistently associated with the coral under a given treatment and the single effects of manipulated eutrophication and overfishing could not predict the combined effect. Our data underlines the importance of conducting field studies in a holobiont framework, taking both, physiological and molecular measures into account.

  12. Distribution and diversity of bacterial secretion systems across metagenomic datasets.

    Science.gov (United States)

    Barret, Matthieu; Egan, Frank; O'Gara, Fergal

    2013-02-01

    Bacteria can manipulate their surrounding environment through the secretion of proteins into other living organisms and into the extracellular milieu. In Gram stain negative bacteria this process is mediated by different types of secretion systems from type I through type VI secretion system (T1SS-T6SS). In this study the prevalence of these secretion systems in 312 publicly available microbiomes derived from a wide range of ecosystems was investigated by a gene-centric approach. Our analysis demonstrates that some secretion systems are over-represented in some specific samples. In addition, some T3SS and T6SS phylogenetic clusters were specifically enriched in particular ecological niches, which could indicate specific bacterial adaptation to these environments. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  13. Investigation of bacterial diversity of hot springs of Odisha, India

    Directory of Open Access Journals (Sweden)

    Rajesh Kumar Sahoo

    2015-12-01

    Full Text Available 16S rRNA deep sequencing analysis, targeting V3 region was performed using Illumina bar coded sequencing. Sediment samples from two hot springs (Atri and Taptapani were collected. Atri and Taptapani metagenomes were classified into 50 and 51 bacterial phyla. Proteobacteria (45.17% dominated the Taptapani sample metagenome followed by Bacteriodetes (23.43% and Cyanobacteria (10.48% while in the Atri sample, Chloroflexi (52.39%, Nitrospirae (10.93% and Proteobacteria (9.98% dominated. A large number of sequences remained taxonomically unresolved in both hot springs, indicating the presence of potentially novel microbes in these two unique habitats thus unraveling the importance of the current study. Metagenome sequence information is now available at NCBI, SRA database accession no. SRP057428.

  14. Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China.

    Science.gov (United States)

    Zhang, Bingchang; Kong, Weidong; Wu, Nan; Zhang, Yuanming

    2016-06-01

    Biological soil crusts (BSCs) are common and play critical roles in semi-arid and arid ecosystems. Bacteria, as an important community in BSCs, play critical roles in biochemical processes. However, how bacterial diversity and community change in different successional stages of BSCs is still unknown. We used 454 pyrosequencing of 16S rRNA to investigate the bacterial composition and community, and the relationships between bacterial composition and environmental factors were also explored. In different successional stages of BSCs, the number of bacteria operational taxonomic units (OTUs) detected in each sample ranged from 2572 to 3157. Proteobacteria, Cyanobacteria, Bacteroidetes were dominant in BSCs, followed by Firmicutes, Acidobacteria, and Actinobacteria. At the successional stages of BSCs, bacterial communities, OTU composition and their relative abundance notably differentiated, and Cyanobacteria, especially Microcoleus vaginatus, dominated algal crust and lichen crust, and were the main C-fixing bacteria in BSCs. Proteobacteria and Bacteroidetes increased with the development of BSCs. OTUs related to Planomicrobium Chinese, Desulfobulbus sp., Desulfomicrobium sp., Arthrobacter sp., and Ahhaerbacter sp. showed higher relative abundance in bare sand than other successional stages of BSCs, while relative abundance of Sphingomonas sp. Niastella sp., Pedobacter, Candidatus solobacter, and Streptophyta increased with the development of BSCs. In successional stages of BSCs, bacterial OTUs composition demonstrated strong correlations with soil nutrients, soil salts, and soil enzymes. Additionally, variation of bacterial composition led to different ecological function. In bare sand, some species were related with mineral metabolism or promoting plant growth, and in algal crust and lichen crust, C-fixing bacteria increased and accumulated C to the desert soil. In later developed stage of BSCs, bacteria related with decomposition of organic matter, such as

  15. Genetic Diversity of Bacterial Communities and Gene Transfer Agents in Northern South China Sea

    Science.gov (United States)

    Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Jiang, Zhao-Yu; Sun, Cui-Ci; Cheng, Hao

    2014-01-01

    Pyrosequencing of the 16S ribosomal RNA gene (rDNA) amplicons was performed to investigate the unique distribution of bacterial communities in northern South China Sea (nSCS) and evaluate community structure and spatial differences of bacterial diversity. Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes constitute the majority of bacteria. The taxonomic description of bacterial communities revealed that more Chroococcales, SAR11 clade, Acidimicrobiales, Rhodobacterales, and Flavobacteriales are present in the nSCS waters than other bacterial groups. Rhodobacterales were less abundant in tropical water (nSCS) than in temperate and cold waters. Furthermore, the diversity of Rhodobacterales based on the gene transfer agent (GTA) major capsid gene (g5) was investigated. Four g5 gene clone libraries were constructed from samples representing different regions and yielded diverse sequences. Fourteen g5 clusters could be identified among 197 nSCS clones. These clusters were also related to known g5 sequences derived from genome-sequenced Rhodobacterales. The composition of g5 sequences in surface water varied with the g5 sequences in the sampling sites; this result indicated that the Rhodobacterales population could be highly diverse in nSCS. Phylogenetic tree analysis result indicated distinguishable diversity patterns among tropical (nSCS), temperate, and cold waters, thereby supporting the niche adaptation of specific Rhodobacterales members in unique environments. PMID:25364820

  16. Fish species composition, diversity and abundance of the lower New ...

    African Journals Online (AJOL)

    A thirteen-week investigation to determine the fish species composition, diversity and abundance of the Lower New Calabar River, in Rivers State, aimed at providing information on the fish stock and their status for documentation, knowledge improvement, and development of conservation and management strategies was ...

  17. Species Richness and Diversity Reveal that Human-Modified ...

    African Journals Online (AJOL)

    Family diversity and richness showed no significant differences across the sites. The spider species consisted of primarily three functional groups: ground wanderers, web builders and plant wanderers, and showed no within-group differences in abundance between sites. Similarity index between the study sites revealed a ...

  18. Phenotypic and genetic diversity of the species Lactobacillus rhamnosus

    NARCIS (Netherlands)

    Ceapa, C.D.

    2016-01-01

    The thesis explores the diversity of Lactobacillus rhamnosus, a species from which strains are studied for their anti-inflammatory, anti-allergic, and diarrhea preventing effects. The work combines observations on the behavior of the bacteria in a simplified laboratory setting (use of

  19. Determinants of orchid species diversity in Latin America

    Czech Academy of Sciences Publication Activity Database

    Štípková, Zuzana; Traxmandlová, Iva; Kindlmann, Pavel

    2016-01-01

    Roč. 16, č. 2 (2016), s. 293-297 ISSN 1409-3871 R&D Projects: GA MŠk(CZ) LO1415; GA ČR GB14-36098G Institutional support: RVO:67179843 Keywords : altitude * habitat diversity * species-area relationship Subject RIV: EF - Botanics

  20. Species diversity variations in Neogene deep-sea benthic

    Indian Academy of Sciences (India)

    Some species of benthic foraminifera are sensitive to changes in water mass properties whereas others are sensitive to organic fluxes and deep-sea oxygenation. Benthic faunal diversity has been found closely linked to food web, bottom water oxygen levels, and substrate and water mass stability. The present study is ...

  1. Species composition, plant cover and diversity of recently reforested ...

    African Journals Online (AJOL)

    SERVER

    2007-12-17

    Dec 17, 2007 ... Deforestation, over-cultivation and rural growth have severely ... over-cultivation, plant populations changed, and biolo- ... Restoring community structure (e.g. species composi-tion ... plant diversity at all spatial scales are the criteria that should ..... taxonomic groups in recovering and restored forests.

  2. Tree species Diversity in the Department of Forest Resources ...

    African Journals Online (AJOL)

    An inventory of trees (>10cm diameter at breast height (dbh)) growing within the premises (~1.2ha) of the Department of Forest Resources Management (DFRM), University of Ibadan, Nigeria, was conducted as a case study of the species quality (richness and diversity) and quantity (volume) found on the University campus.

  3. Comparative genomics of Wolbachia and the bacterial species concept.

    Directory of Open Access Journals (Sweden)

    Kirsten Maren Ellegaard

    2013-04-01

    Full Text Available The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally

  4. Species Diversity and Bird Feed in Residential Complex

    Science.gov (United States)

    Hadinoto; Suhesti, Eni

    2017-12-01

    Bird is one component of the ecosystem which has an important role in supporting the occurrence of an organism's life cycle. Therefore, the presence of birds in an area is important, because it can affect the existence and distribution of plant species. The purpose of this study is to calculate the diversity of bird species and identify the source of bird feed in the compound. This study was conducted by field surveys in the residential complex. In addition to the birds as a research object vegetation as habitat / foraging birds were also observed. Data were analyzed by using the bird diversity index, richenes index, bundance index, dominance analysis, analysis of bird distribution and analysis of the level of meeting types, while vegetation will be analyzed based on the type and part of what is eaten by birds. In Pandau Jaya housing complex, found as many as 12 species of birds which consists of seven families. Bird species often present is Cucak Kutilang (Pycnonotus aurigaster) of 20 individuals, Bondol Peking (Lonchura punctulata) 14 individuals and Perkutut Jawa (Geopelia striata) 10 individuals. Bird species diversity (H ‘) in Pandau Jaya housing complex is still relatively moderate with a value of 2.27, while the Evenness Index (E) of 0.91 and Richenes Index (R) of 2.45. Types of vegetation as a food source, among others: mango, guava, cherry, jackfruit, ketapang, coconut, areca, palm, banana, papaya, flowers and grasses.

  5. Petroleum-influenced beach sediments of the campeche bank, Mexico: Diversity and bacterial community structure assessment

    Energy Technology Data Exchange (ETDEWEB)

    Rosano-Hernandez, M. C.; Ramirez-Saad, H.; Fernandez-Linares, L.; Xoconostle, B.

    2009-07-01

    In Mexican, either spilled or seeped out petroleum impacts nearly 300 km of the beach between Dos Bocas (Tabasco State) to Champoton town (Campeche State), where between 9 to exceptionally 9 to exceptionally 300 tonnes of oil as tar balls have been measured. This study was focused to explore, for the first time, the bacterial diversity and community structure ({alpha}-diversity)- in a kilometric scale on petroleum influenced sediments of 100 km of sandy beach. (Author)

  6. Petroleum-influenced beach sediments of the campeche bank, Mexico: Diversity and bacterial community structure assessment

    International Nuclear Information System (INIS)

    Rosano-Hernandez, M. C.; Ramirez-Saad, H.; Fernandez-Linares, L.; Xoconostle, B.

    2009-01-01

    In Mexican, either spilled or seeped out petroleum impacts nearly 300 km of the beach between Dos Bocas (Tabasco State) to Champoton town (Campeche State), where between 9 to exceptionally 9 to exceptionally 300 tonnes of oil as tar balls have been measured. This study was focused to explore, for the first time, the bacterial diversity and community structure (α-diversity)- in a kilometric scale on petroleum influenced sediments of 100 km of sandy beach. (Author)

  7. Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time.

    Science.gov (United States)

    Nguyen, Ngoc-Lan; Kim, Yeon-Ju; Hoang, Van-An; Subramaniyam, Sathiyamoorthy; Kang, Jong-Pyo; Kang, Chang Ho; Yang, Deok-Chun

    2016-01-01

    Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil.

  8. Multifaceted diversity-area relationships reveal global hotspots of mammalian species, trait and lineage diversity.

    Science.gov (United States)

    Mazel, Florent; Guilhaumon, François; Mouquet, Nicolas; Devictor, Vincent; Gravel, Dominique; Renaud, Julien; Cianciaruso, Marcus Vinicius; Loyola, Rafael Dias; Diniz-Filho, José Alexandre Felizola; Mouillot, David; Thuiller, Wilfried

    2014-08-01

    To define biome-scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them to 'classical' hotspots based on species richness (SR) only. Global. SR, PD & FD were computed for 782 terrestrial ecoregions using distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework that incorporates the species relative coverage in each ecoregion. We build large-scale multifaceted diversity-area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each diversity facet. Finally we defined hotspots as the top-ranked ecoregions. While ignoring species relative coverage led to a relative good congruence between biome top ranked SR, PD and FD hotspots, ecoregions harboring a rich and abundantly represented evolutionary history and functional diversity did not match with top ranked ecoregions defined by species richness. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than species richness as a function of area. The fact that PD/FD reach faster their maximal value than SR may suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it is quantified at global scale and should have important consequences in conservation. Incorporating species relative coverage into the delineation of multifaceted hotspots of diversity lead to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail at preserving those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at global scale.

  9. Diversity of bacterial communities on the facial skin of different age-group Thai males

    Directory of Open Access Journals (Sweden)

    Alisa Wilantho

    2017-11-01

    national biogeography, revealed differences in the distribution pattern of species, although common bacteria were present in both biogeographical samples. Furthermore, B-RISA served as a crosscheck result to the 16S rRNA gene sequencing (i.e., differences between teenage and elderly microbiota. Conclusions This study revealed and compared the microbial diversity on different aged Thai male faces, and included analyses for representing the bacterial flora, the clinical skin characteristics, and comparison with the US age-matched. The results represent the first skin microbiota of Thai males, and helps the design of a large-scale skin microbiome study of Thais. The findings of the diversity among ages, skin type and national biogeography supported the importance of these traits in the skin microbiome and in developing a safe and sustainable treatment for acne and aging skin diseases.

  10. Catecholamines and in vitro growth of pathogenic bacteria: enhancement of growth varies greatly among bacterial species

    Science.gov (United States)

    Belay, Tesfaye; Aviles, Hernan; Vance, Monique; Fountain, Kimberly; Sonnenfeld, Gerald

    2003-01-01

    The purpose of this study was to examine the effects of catecholamines on in vitro growth of a range of bacterial species, including anaerobes. Bacteria tested included: Porphyromonas gingivalis, Bacteriodes fragilis, Shigella boydii, Shigella sonnie, Enterobacter Sp, and Salmonella choleraesuis. The results of the current study indicated that supplementation of bacterial cultures in minimal medium with norepinephrine or epinephrine did not result in increased growth of bacteria. Positive controls involving treatment of Escherichia coli with catecholamines did result in increased growth of that bacterial species. The results of the present study extend previous observations that showed differential capability of catecholamines to enhance bacterial growth in vitro.

  11. Bacterial diversity in oil-polluted marine coastal sediments.

    Science.gov (United States)

    Acosta-González, Alejandro; Marqués, Silvia

    2016-04-01

    Marine environments harbour a persistent microbial seed which can be shaped by changes of the environmental conditions such as contamination by petroleum components. Oil spills, together with small but continuous discharges of oil from transportation and recreational activities, are important sources of hydrocarbon pollution within the marine realm. Consequently, prokaryotic communities have become well pre-adapted toward oil pollution, and many microorganisms that are exposed to its presence develop an active degradative response. The natural attenuation of oil pollutants, as has been demonstrated in many sites, is modulated according to the intrinsic environmental properties such as the availability of terminal electron acceptors and elemental nutrients, together with the degree of pollution and the type of hydrocarbon fractions present. Whilst dynamics in the bacterial communities in the aerobic zones of coastal sediments are well characterized and the key players in hydrocarbon biodegradation have been identified, the subtidal ecology of the anaerobic community is still not well understood. However, current data suggest common patterns of response in these ecosystems. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Bacterial flagellar capping proteins adopt diverse oligomeric states

    Energy Technology Data Exchange (ETDEWEB)

    Postel, Sandra; Deredge, Daniel; Bonsor, Daniel A.; Yu, Xiong; Diederichs, Kay; Helmsing, Saskia; Vromen, Aviv; Friedler, Assaf; Hust, Michael; Egelman, Edward H.; Beckett, Dorothy; Wintrode, Patrick L.; Sundberg, Eric J. (UV); (Braunschweig); (Maryland-MED); (Konstanz); (Maryland); (Hebrew)

    2016-09-24

    Flagella are crucial for bacterial motility and pathogenesis. The flagellar capping protein (FliD) regulates filament assembly by chaperoning and sorting flagellin (FliC) proteins after they traverse the hollow filament and exit the growing flagellum tip. In the absence of FliD, flagella are not formed, resulting in impaired motility and infectivity. Here, we report the 2.2 Å resolution X-ray crystal structure of FliD fromPseudomonas aeruginosa, the first high-resolution structure of any FliD protein from any bacterium. Using this evidence in combination with a multitude of biophysical and functional analyses, we find thatPseudomonasFliD exhibits unexpected structural similarity to other flagellar proteins at the domain level, adopts a unique hexameric oligomeric state, and depends on flexible determinants for oligomerization. Considering that the flagellin filaments on which FliD oligomers are affixed vary in protofilament number between bacteria, our results suggest that FliD oligomer stoichiometries vary across bacteria to complement their filament assemblies.

  13. Distribution of 10 periodontal bacterial species in children and adolescents over a 7-year period.

    Science.gov (United States)

    Nakano, K; Miyamoto, E; Tamura, K; Nemoto, H; Fujita, K; Nomura, R; Ooshima, T

    2008-10-01

    There is scant information available regarding the distribution of periodontal bacterial species in children and adolescents over an extended period. The purpose of this study was to compare bacterial profiles in the same individuals over a period of 7 years. Twenty-six children and adolescents from whom dental plaque and saliva specimens were obtained during both the first (1999-2000) and second (2006-2007) periods, were analyzed. Bacterial DNA was extracted from each specimen and the presence of 10 periodontal bacterial species was determined using a PCR method, with a focus on the red complex species of Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia. Subjects with red complex species in saliva specimens obtained during the second collection possessed a significantly higher number of total bacterial species than those without. The detection rate of the red complex species in the second collection period samples was significantly greater in subjects who had two or more species detected in samples taken during the first collection compared with the other subjects. Subjects possessing red complex species may be at possible risk for infection with a high number of periodontal bacterial species during adolescent and younger adult years.

  14. Analyzing fractal property of species abundance distribution and diversity indexes.

    Science.gov (United States)

    Su, Qiang

    2016-03-07

    Community diversity is usually characterized by numerical indexes; however it indeed depends on the species abundance distribution (SAD). Diversity indexes and SAD are based on the same information but treating as separate themes. Ranking species abundance from largest to smallest, the decreasing pattern can give the information about the SAD. Frontier proposed such SAD might be a fractal structure, and first applied the Zipf-Mandelbrot model to the SAD study. However, this model fails to include the Zipf model, and also fails to ensure an integer rank. In this study, a fractal model of SAD was reconstructed, and tested with 104 community samples from 8 taxonomic groups. The results show that there was a good fit of the presented model. Fractal parameter (p) determines the SAD of a community. The ecological significance of p relates to the "dominance" of a community. The correlation between p and classical diversity indexes show that Shannon index decreases and Simpson index increases as p increases. The main purpose of this paper is not to compare with other SADs models; it simply provides a new interpretation of SAD model construction, and preliminarily integrates diversity indexes and SAD model into a broader perspective of community diversity. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Influence of long-term land application of class B biosolids on soil bacterial diversity

    Science.gov (United States)

    This project evaluated the influence of annual land applications of Class B biosolids on soil bacterial diversity monitored over a 20 year period. Each annual land application was followed by a cotton crop. The study was initiated in 1986 at the University of Arizona Marana Agricultural Center, 21 m...

  16. Bacterial diversity in a tropical crude oil-polluted soil undergoing ...

    African Journals Online (AJOL)

    The bacterial diversity in a tropical soil experimentally polluted with crude oil during a 57 days bioremediation was investigated in five 1 m2 plots using total culturable hydrocarbon utilizing bacteria, heterotrophic bacteria and gas chromatographic analyses. Four out of the five experimental plots received each 4 L of Bonny ...

  17. Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity

    Science.gov (United States)

    Rabbi, S. M. F.; Daniel, H.; Lockwood, P. V.; MacDonald, C.; Pereg, L.; Tighe, M.; Wilson, B. R.; Young, I. M.

    2016-09-01

    Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250-2000 μm) and micro-aggregates (53-250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes.

  18. An exactly solvable coarse-grained model for species diversity

    Science.gov (United States)

    Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

    2012-07-01

    We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology.

  19. An exactly solvable coarse-grained model for species diversity

    International Nuclear Information System (INIS)

    Suweis, Samir; Maritan, Amos; Rinaldo, Andrea

    2012-01-01

    We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth–death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology. (paper)

  20. Neotropical bats: estimating species diversity with DNA barcodes.

    Directory of Open Access Journals (Sweden)

    Elizabeth L Clare

    Full Text Available DNA barcoding using the cytochrome c oxidase subunit 1 gene (COI is frequently employed as an efficient method of species identification in animal life and may also be used to estimate species richness, particularly in understudied faunas. Despite numerous past demonstrations of the efficiency of this technique, few studies have attempted to employ DNA barcoding methodologies on a large geographic scale, particularly within tropical regions. In this study we survey current and potential species diversity using DNA barcodes with a collection of more than 9000 individuals from 163 species of Neotropical bats (order Chiroptera. This represents one of the largest surveys to employ this strategy on any animal group and is certainly the largest to date for land vertebrates. Our analysis documents the utility of this tool over great geographic distances and across extraordinarily diverse habitats. Among the 163 included species 98.8% possessed distinct sets of COI haplotypes making them easily recognizable at this locus. We detected only a single case of shared haplotypes. Intraspecific diversity in the region was high among currently recognized species (mean of 1.38%, range 0-11.79% with respect to birds, though comparable to other bat assemblages. In 44 of 163 cases, well-supported, distinct intraspecific lineages were identified which may suggest the presence of cryptic species though mean and maximum intraspecific divergence were not good predictors of their presence. In all cases, intraspecific lineages require additional investigation using complementary molecular techniques and additional characters such as morphology and acoustic data. Our analysis provides strong support for the continued assembly of DNA barcoding libraries and ongoing taxonomic investigation of bats.

  1. Phytoplankton production systems in a shellfish hatchery: variations of the bacterial load and diversity of vibrios.

    Science.gov (United States)

    Dubert, J; Fernández-Pardo, A; Nóvoa, S; Barja, J L; Prado, S

    2015-06-01

    Outbreaks of disease caused by some Vibrio species represent the main production bottleneck in shellfish hatcheries. Although the phytoplankton used as food is one of the main sources of bacteria, studies of the associated bacterial populations, specifically vibrios, are scarce. The aim of the study was the microbiological monitoring of the microalgae as the first step in assessing the risk disease for bivalve cultures. Two phytoplankton production systems were sampled weekly throughout 1-year period in a bivalve hatchery. Quantitative analysis revealed high levels of marine heterotrophic bacteria in both systems throughout the study. Presumptive vibrios were detected occasionally and at low concentrations. In most of the cases, they belonged to the Splendidus and Harveyi clades. The early detection of vibrios in the microalgae may be the key for a successful bivalve culture. Their abundance and diversity were affected by factors related to the hatchery environment. This work represents the first long study where the presence of vibrios was evaluated rigorously in phytoplankton production systems and provides a suitable microbiological protocol to control and guarantee the quality of the algal cultures to avoid the risk of transferring potential pathogens to shellfish larvae and/or broodstock. © 2015 The Society for Applied Microbiology.

  2. Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.

    Directory of Open Access Journals (Sweden)

    Koen Illeghems

    Full Text Available This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni. Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.

  3. The rhizosphere and PAH amendment mediate impacts on functional and structural bacterial diversity in sandy peat soil

    International Nuclear Information System (INIS)

    Yrjaelae, Kim; Keskinen, Anna-Kaisa; Akerman, Marja-Leena; Fortelius, Carola; Sipilae, Timo P.

    2010-01-01

    To reveal the degradation capacity of bacteria in PAH polluted soil and rhizosphere we combined bacterial extradiol ring-cleavage dioxygenase and 16S rRNA analysis in Betula pubescens rhizoremediation. Characterisation of the functional bacterial community by RFLP revealed novel environmental dioxygenases, and their putative hosts were studied by 16S rRNA amplification. Plant rhizosphere and PAH amendment effects were detected by the RFLP/T-RFLP analysis. Functional species richness increased in the birch rhizosphere and PAH amendment impacted the compositional diversity of the dioxygenases and the structural 16S rRNA community. A shift from an Acidobacteria and Verrucomicrobia dominated to an Alpha- and Betaproteobacteria dominated community structure was detected in polluted soil. Clone sequence analysis indicated catabolic significance of Burkholderia in PAH polluted soil. These results advance our understanding of rhizoremediation and unveil the extent of uncharacterized functional bacteria to benefit bioremediation by facilitating the development of the molecular tool box to monitor bacterial populations in biodegradation. - The bacterial community analysis using 16S rRNA and extradiol dioxygenase marker genes in rhizoremediation revealed both a rhizosphere and a PAH-pollution effect.

  4. Pig Farmers' Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes.

    Science.gov (United States)

    Vestergaard, Ditte V; Holst, Gitte J; Basinas, Ioannis; Elholm, Grethe; Schlünssen, Vivi; Linneberg, Allan; Šantl-Temkiv, Tina; Finster, Kai; Sigsgaard, Torben; Marshall, Ian P G

    2018-01-01

    Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building's occupants. A major example is the decreased diversity and altered composition of indoor airborne microbial communities as a proposed explanation for the increasing prevalence of asthma and allergies worldwide. Previous research has shown that living on a farm confers protection against development of asthma and allergies, with airborne bacteria suggested as playing a role in this protective effect. However, the composition of this beneficial microbial community has still not been identified. We sampled settled airborne dust using a passive dust sampler from Danish pig stables, associated farmers' homes, and from suburban homes (267 samples in total) and carried out quantitative PCR measurements of bacterial abundance and MiSeq sequencing of the V3-V4 region of bacterial 16S rRNA genes found in these samples. Airborne bacteria had a greater diversity and were significantly more abundant in pig stables and farmers' homes than suburban homes (Wilcoxon rank sum test P < 0.05). Moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers' homes than in suburban homes (ALDEx2 with P < 0.05), including Firmicutes, Peptostreptococcaceae, Prevotellaceae, Lachnospiraceae, Ruminococcaceae, Ruminiclostridium , and Lactobacillus . Pig stables had significantly lower airborne bacterial diversity than farmers' homes, and there was no discernable direct transfer of airborne bacteria from stable to home. This study identifies differences in indoor airborne bacterial communities that may be an important component of this putative protective effect, while showing that pig stables themselves do not appear to

  5. Bacterial Human Virulence Genes across Diverse Habitats As Assessed by In silico Analysis of Environmental Metagenomes

    DEFF Research Database (Denmark)

    Søborg, Ditte A; Hendriksen, Niels B; Kilian, Mogens

    2016-01-01

    of natural environments in the evolution of bacterial virulence. Twenty four bacterial virulence genes were analyzed in 46 diverse environmental metagenomic datasets, representing various soils, seawater, freshwater, marine sediments, hot springs, the deep-sea, hypersaline mats, microbialites, gutless worms......The occurrence and distribution of clinically relevant bacterial virulence genes across natural (non-human) environments is not well understood. We aimed to investigate the occurrence of homologs to bacterial human virulence genes in a variety of ecological niches to better understand the role...... in non-human environments point to an important ecological role of the genes for the activity and survival of environmental bacteria. Furthermore, the high degree of sequence conservation between several of the environmental and clinical genes suggests common ancestral origins....

  6. Diversity of pufM genes, involved in aerobic anoxygenic photosynthesis, in the bacterial communities associated with colonial ascidians.

    Science.gov (United States)

    Martínez-García, Manuel; Díaz-Valdés, Marta; Antón, Josefa

    2010-03-01

    Ascidians are invertebrate filter feeders widely distributed in benthic marine environments. A total of 14 different ascidian species were collected from the Western Mediterranean and their bacterial communities were analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene. Results showed that ascidian tissues harbored Bacteria belonging to Gamma- and Alphaproteobacteria classes, some of them phylogenetically related to known aerobic anoxygenic phototrophs (AAPs), such as Roseobacter sp. In addition, hierarchical cluster analysis of DGGE patterns showed a large variability in the bacterial diversity among the different ascidians analyzed, which indicates that they would harbor different bacterial communities. Furthermore, pufM genes, involved in aerobic anoxygenic photosynthesis in marine and freshwater systems, were widely detected within the ascidians analyzed, because nine out of 14 species had pufM genes inside their tissues. The pufM gene was only detected in those specimens that inhabited shallow waters (<77 m of depth). Most pufM gene sequences were very closely related to that of uncultured marine bacteria. Thus, our results suggest that the association of ascidians with bacteria related to AAPs could be a general phenomenon and that ascidian-associated microbiota could use the light that penetrates through the tunic tissue as an energy source.

  7. Bio-Prospecting Laccases in the Bacterial Diversity of Activated Sludge From Pulp and Paper Industry.

    Science.gov (United States)

    Gupta, Vijaya; Capalash, Neena; Gupta, Naveen; Sharma, Prince

    2017-03-01

    Activated sludge is an artificial ecosystem known to harbor complex microbial communities. Bacterial diversity in activated sludge from pulp and paper industry was studied to bioprospect for laccase, the multicopper oxidase applicable in a large number of industries due to its ability to utilize a wide range of substrates. Bacterial diversity using 454 pyrosequencing and laccase diversity using degenerate primers specific to conserved copper binding domain of laccase like multicopper oxidase (LMCO) genes were investigated. 1231 OTUs out of 11,425 sequence reads for bacterial diversity and 11 OTUs out of 15 reads for LMCO diversity were formed. Phylum Proteobacteria (64.95 %) with genus Thauera (13.65 %) was most abundant followed by phylum Bacteriodetes (11.46 %) that included the dominant genera Paludibacter (1.93 %) and Lacibacter (1.32 %). In case of LMCOs, 40 % sequences showed affiliation with Proteobacteria and 46.6 % with unculturable bacteria, indicating considerable novelty, and 13.3 % with Bacteroidetes. LMCOs belonged to H and J families.

  8. Long-term organic-inorganic fertilization ensures great soil productivity and bacterial diversity after natural-to-agricultural ecosystem conversion.

    Science.gov (United States)

    Xun, Weibing; Xu, Zhihui; Li, Wei; Ren, Yi; Huang, Ting; Ran, Wei; Wang, Boren; Shen, Qirong; Zhang, Ruifu

    2016-09-01

    Natural ecosystems comprise the planet's wild plant and animal resources, but large tracts of land have been converted to agroecosystems to support the demand for agricultural products. This conversion limits the number of plant species and decreases the soil biological diversity. Here we used high-throughput 16S rRNA gene sequencing to evaluate the responses of soil bacterial communities in long-term converted and fertilized red soils (a type of Ferralic Cambisol). We observed that soil bacterial diversity was strongly affected by different types of fertilization management. Oligotrophic bacterial taxa demonstrated large relative abundances in chemically fertilized soil, whereas copiotrophic bacterial taxa were found in large relative abundances in organically fertilized and fallow management soils. Only organic-inorganic fertilization exhibited the same local taxonomic and phylogenetic diversity as that of a natural ecosystem. However, the independent use of organic or inorganic fertilizer reduced local taxonomic and phylogenetic diversity and caused biotic homogenization. This study demonstrated that the homogenization of bacterial communities caused by natural-to-agricultural ecosystem conversion can be mitigated by employing rational organic-inorganic fertilization management.

  9. Are Tree Species Diversity and Genotypic Diversity Effects on Insect Herbivores Mediated by Ants?

    Directory of Open Access Journals (Sweden)

    María José Campos-Navarrete

    Full Text Available Plant diversity can influence predators and omnivores and such effects may in turn influence herbivores and plants. However, evidence for these ecological feedbacks is rare. We evaluated if the effects of tree species (SD and genotypic diversity (GD on the abundance of different guilds of insect herbivores associated with big-leaf mahogany (Swietenia macrophylla were contingent upon the protective effects of ants tending extra-floral nectaries of this species. This study was conducted within a larger experiment consisting of mahogany monocultures and species polycultures of four species and -within each of these two plot types- mahogany was represented by either one or four maternal families. We selected 24 plots spanning these treatment combinations, 10 mahogany plants/plot, and within each plot experimentally reduced ant abundance on half of the selected plants, and surveyed ant and herbivore abundance. There were positive effects of SD on generalist leaf-chewers and sap-feeders, but for the latter group this effect depended on the ant reduction treatment: SD positively influenced sap-feeders under ambient ant abundance but had no effect when ant abundance was reduced; at the same time, ants had negative effects on sap feeders in monoculture but no effect in polyculture. In contrast, SD did not influence specialist stem-borers or leaf-miners and this effect was not contingent upon ant reduction. Finally, GD did not influence any of the herbivore guilds studied, and such effects did not depend on the ant treatment. Overall, we show that tree species diversity influenced interactions between a focal plant species (mahogany and ants, and that such effects in turn mediated plant diversity effects on some (sap-feeders but not all the herbivores guilds studied. Our results suggest that the observed patterns are dependent on the combined effects of herbivore identity, diet breadth, and the source of plant diversity.

  10. Unrecognized coral species diversity masks differences in functional ecology.

    Science.gov (United States)

    Boulay, Jennifer N; Hellberg, Michael E; Cortés, Jorge; Baums, Iliana B

    2014-02-07

    Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P. lobata reproduces mainly sexually, P. evermanni dominates in areas where triggerfish prey on bioeroding mussels living within the coral skeleton, thereby generating asexual coral fragments. These fragments proliferate in marginal habitat not colonized by P. lobata. The two Porites species also show a differential bleaching response despite hosting the same dominant symbiont subclade. Thus, hidden diversity within these reef-builders has until now obscured differences in trophic interactions, reproductive dynamics and bleaching susceptibility, indicative of differential responses when confronted with future climate change.

  11. Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

    Science.gov (United States)

    Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2014-06-01

    To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

  12. Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke

    Science.gov (United States)

    Yang, Hui; Hu, Jinxiang; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-02-01

    The interaction between roots and bacterial communities in halophytic species is poorly understood. Here, we used Jerusalem artichoke cultivar Nanyu 1 (NY-1) to characterise root distribution patterns and determine diversity and abundance of bacteria in the rhizosphere soil under variable salinity. Root growth was not inhibited within the salinity range 1.2 to 1.9 g salt/kg, but roots were mainly confined to 0-20 cm soil layer vertically and 0-30 cm horizontally from the plant centre. Root concentrations of K+, Na+, Mg2+ and particularly Ca2+ were relatively high under salinity stress. High salinity stress decreased soil invertase and catalase activity. Using a next-generation, Illumina-based sequencing approach, we determined higher diversity of bacteria in the rhizosphere soil at high than low salinity. More than 15,500 valid reads were obtained, and Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria predominated in all samples, accounting for >80% of the reads. On a genus level, 636 genera were common to the low and high salinity treatments at 0-5 cm and 5-10 cm depth. The abundance of Steroidobacter and Sphingomonas was significantly decreased by increasing salinity. Higher Shannon and Chao 1 indices with increasing severity of salt stress indicated that high salt stress increased diversity in the bacterial communities.

  13. SALMONELLA SPECIE AND TOTAL VIABLE BACTERIAL LOAD IN ROASTED CHICKENS SOLD IN JOS-NIGERIA

    OpenAIRE

    Carol Okoli; Okonji M.C; Ugoh S.C; Okolo S.N; Okoli A.C; Alu A.J

    2007-01-01

    The study was to investigate for the presence of Salmonella specie and total viable aerobic bacterial load in roasted chickens sold in Jos. The study was carried out on twenty five chicken samples. No salmonella specie was isolated from the samples. However, other bacterial organisms were isolates, viz: 9(36%) of the samples yielded E.coli; 5(20%) yielded Citobacter species; 3(12%) yielded Proteus species and 6(24%) yielded Klebsiella species while 2(8%) showed no growth. An average total via...

  14. Differential iridoid production as revealed by a diversity panel of 84 cultivated and wild blueberry species.

    Science.gov (United States)

    Leisner, Courtney P; Kamileen, Mohamed O; Conway, Megan E; O'Connor, Sarah E; Buell, C Robin

    2017-01-01

    Cultivated blueberry (Vaccinium corymbosum, Vaccinium angustifolium, Vaccinium darrowii, and Vaccinium virgatum) is an economically important fruit crop native to North America and a member of the Ericaceae family. Several species in the Ericaceae family including cranberry, lignonberry, bilberry, and neotropical blueberry species have been shown to produce iridoids, a class of pharmacologically important compounds present in over 15 plant families demonstrated to have a wide range of biological activities in humans including anti-cancer, anti-bacterial, and anti-inflammatory. While the antioxidant capacity of cultivated blueberry has been well studied, surveys of iridoid production in blueberry have been restricted to fruit of a very limited number of accessions of V. corymbosum, V. angustifolium and V. virgatum; none of these analyses have detected iridoids. To provide a broader survey of iridoid biosynthesis in cultivated blueberry, we constructed a panel of 84 accessions representing a wide range of cultivated market classes, as well as wild blueberry species, and surveyed these for the presence of iridoids. We identified the iridoid glycoside monotropein in fruits and leaves of all 13 wild Vaccinium species, yet only five of the 71 cultivars. Monotropein positive cultivars all had recent introgressions from wild species, suggesting that iridoid production can be targeted through breeding efforts that incorporate wild germplasm. A series of diverse developmental tissues was also surveyed in the diversity panel, demonstrating a wide range in iridoid content across tissues. Taken together, this data provides the foundation to dissect the molecular and genetic basis of iridoid production in blueberry.

  15. The richness and diversity of Lepidoptera species in different ...

    African Journals Online (AJOL)

    The family Nymphalidae was the most dominant one in the parc with 32.48%. The diversity index (H' and H'max) and the equitability (E) calculated for the 6 types of habitats is H'= 2,74 bits, H'max = 4,09 bits and E = 0,67 bits, meaning that the Lepidoptera species are at equilibrium with the different types of habitat which ...

  16. Disturbance, Functional Diversity and Ecosystem Processes: Does Species Identity Matter?

    OpenAIRE

    Emrick III, Verl Roy

    2013-01-01

    The role of disturbance is widely recognized as a fundamental driver of ecological organization from individual species to entire landscapes. Anthropogenic disturbances from military training provide a unique opportunity to examine effects of disturbance on vegetation dynamics, physicochemical soil properties, and ecosystem processes. Additionally, plant functional diversity has been suggested as the key to ecosystem processes such as productivity and nutrient dynamics. I investigated how dis...

  17. Determinants of orchid species diversity in world islands

    Czech Academy of Sciences Publication Activity Database

    Traxmandlová, Iva; Ackerman, J. D.; Tremblay, R. L.; Roberts, D.L.; Štípková, Zuzana; Kindlmann, Pavel

    2018-01-01

    Roč. 217, č. 1 (2018), s. 12-15 ISSN 0028-646X R&D Projects: GA MŠk(CZ) LO1415; GA ČR GB14-36098G Institutional support: RVO:86652079 Keywords : habitat diversity * island biogeography * latitude * Orchidaceae * species richness * species–area relationship Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 7.330, year: 2016

  18. Bacterial species colonizing the vagina of healthy women are not associated with race.

    Science.gov (United States)

    Beamer, May A; Austin, Michele N; Avolia, Hilary A; Meyn, Leslie A; Bunge, Katherine E; Hillier, Sharon L

    2017-06-01

    The vaginal microbiota of 36 white versus 25 black asymptomatic women were compared using both cultivation-dependent and -independent identification. Significant differences by race were found in colonization and density of bacterial species. However, exclusion of 12 women with bacterial vaginosis by Nugent criteria resulted in no significant differences by race. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin.

    Science.gov (United States)

    Medina, Daniel; Walke, Jenifer B; Gajewski, Zachary; Becker, Matthew H; Swartwout, Meredith C; Belden, Lisa K

    2017-01-01

    One current challenge in microbial ecology is elucidating the functional roles of the large diversity of free-living and host-associated bacteria identified by culture-independent molecular methods. Importantly, the characterization of this immense bacterial diversity will likely require merging data from culture-independent approaches with work on bacterial isolates in culture. Amphibian skin bacterial communities have become a recent focus of work in host-associated microbial systems due to the potential role of these skin bacteria in host defense against the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which is associated with global amphibian population declines and extinctions. As there is evidence that some skin bacteria may inhibit growth of Bd and prevent infection in some cases, there is interest in using these bacteria as probiotic therapy for conservation of at-risk amphibians. In this study, we used skin swabs from American toads ( Anaxyrus americanus ) to: (1) assess the diversity and community structure of culturable amphibian skin bacteria grown on high and low nutrient culture media, (2) determine which culture media recover the highest proportion of the total skin bacterial community of individual toads relative to culture-independent data, and (3) assess whether the plated communities from the distinct media types vary in their ability to inhibit Bd growth in in-vitro assays. Overall, we found that culture media with low nutrient concentrations facilitated the growth of more diverse bacterial taxa and grew distinct communities relative to media with higher nutrient concentrations. Use of low nutrient media also resulted in culturing proportionally more of the bacterial diversity on individual toads relative to the overall community defined using culture-independent methods. However, while there were differences in diversity among media types, the variation among individual hosts was greater than variation among media types, suggesting

  20. Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species

    Directory of Open Access Journals (Sweden)

    Isabelle Laforest-Lapointe

    2016-08-01

    Full Text Available Background The diversity and composition of the microbial community of tree leaves (the phyllosphere varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada. Methods We targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height, the four cardinal points of mid-canopy (2–4 m height, and the top-canopy (4–6 m height. We also collected bottom-canopy leaves from five additional trees from each species. Results Based on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32% and canopy location (6%. Discussion Our results suggest that

  1. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.; Yang, J.; Bougouffa, S.; Wang, Y.; Batang, Zenon B.; Tian, R.; Al-Suwailem, A.; Qian, P.-Y.

    2012-01-01

    -pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than

  2. Characterization of bacterial diversity associated with deep sea ferromanganese nodules from the South China Sea.

    Science.gov (United States)

    Zhang, De-Chao; Liu, Yan-Xia; Li, Xin-Zheng

    2015-09-01

    Deep sea ferromanganese (FeMn) nodules contain metallic mineral resources and have great economic potential. In this study, a combination of culture-dependent and culture-independent (16S rRNA genes clone library and pyrosequencing) methods was used to investigate the bacterial diversity in FeMn nodules from Jiaolong Seamount, the South China Sea. Eleven bacterial strains including some moderate thermophiles were isolated. The majority of strains belonged to the phylum Proteobacteria; one isolate belonged to the phylum Firmicutes. A total of 259 near full-length bacterial 16S rRNA gene sequences in a clone library and 67,079 valid reads obtained using pyrosequencing indicated that members of the Gammaproteobacteria dominated, with the most abundant bacterial genera being Pseudomonas and Alteromonas. Sequence analysis indicated the presence of many organisms whose closest relatives are known manganese oxidizers, iron reducers, hydrogen-oxidizing bacteria and methylotrophs. This is the first reported investigation of bacterial diversity associated with deep sea FeMn nodules from the South China Sea.

  3. Bacterial Diversity in Submarine Groundwater along the Coasts of the Yellow Sea.

    Science.gov (United States)

    Ye, Qi; Liu, Jianan; Du, Jinzhou; Zhang, Jing

    2015-01-01

    Submarine groundwater (SGD) is one of the most significant pathways for the exchange of groundwater and/or source of nutrients, metals and carbon to the ocean, subsequently cause deleterious impacts on the coastal ecosystems. Microorganisms have been recognized as the important participators in the biogeochemical processes in the SGD. In this study, by utilizing 16S rRNA-based Illumina Miseq sequencing technology, we investigated bacterial diversity and distribution in both fresh well water and brackish recirculated porewater along the coasts in the Yellow Sea. The results showed that Actinobacteria and Betaproteobacteria, especially Comamonas spp. and Limnohabitans spp. were dominated in fresh well samples. Distinct patterns of bacterial communities were found among the porewater samples due to different locations, for examples, Cyanbacteria was the most abundant in the porewater samples far from the algal bloomed areas. The analysis of correlation between representative bacterial taxonomic groups and the contexture environmental parameters showed that fresh well water and brackish porewater might provide different nutrients to the coastal waters. Potential key bacterial groups such as Comamonas spp. may be excellent candidates for the bioremediation of the natural pollutants in the SGD. Our comprehensive understanding of bacterial diversity in the SGD along the coasts of the Yellow Sea will create a basis for designing the effective clean-up approach in-situ, and provide valuable information for the coastal management.

  4. Bacterial Diversity in Submarine Groundwater along the Coasts of the Yellow Sea

    Directory of Open Access Journals (Sweden)

    Qi eYe

    2016-01-01

    Full Text Available Submarine groundwater (SGD is one of the most significant pathways for the exchange of groundwater and/or source of nutrients, metals and carbon to the ocean, subsequently cause deleterious impacts on the coastal ecosystems. Microorganisms have been recognized as the important participators in the biogeochemical processes in the SGD. In this study, by utilizing 16S rRNA-based Illumina Miseq sequencing technology, we investigated bacterial diversity and distribution in both fresh well water and brackish recirculated porewater along the coasts in the Yellow Sea. The results showed that Actinobacteria and Betaproteobacteria, especially Comamonas spp. and Limnohabitans spp. were dominated in fresh well samples. Distinct patterns of bacterial communities were found among the porewater samples due to different locations, for examples, Cyanbacteria was the most abundant in the porewater samples far from the algal bloomed areas. The analysis of correlation between representative bacterial taxonomic groups and the contexture environmental parameters showed that fresh well water and brackish porewater might provide different nutrients to the coastal waters. Potential key bacterial groups such as Comamonas spp. may be excellent candidates for the bioremediation of the natural pollutants in the SGD. Our comprehensive understanding of bacterial diversity in the SGD along the coasts of the Yellow Sea will create a basis for designing the effective clean-up approach in-situ, and provide valuable information for the coastal management.

  5. Season, Irrigation, Leaf Age, and Escherichia coli Inoculation Influence the Bacterial Diversity in the Lettuce Phyllosphere

    Science.gov (United States)

    Williams, Thomas R.; Moyne, Anne-Laure; Harris, Linda J.; Marco, Maria L.

    2013-01-01

    The developmental and temporal succession patterns and disturbance responses of phyllosphere bacterial communities are largely unknown. These factors might influence the capacity of human pathogens to persist in association with those communities on agriculturally-relevant plants. In this study, the phyllosphere microbiota was identified for Romaine lettuce plants grown in the Salinas Valley, CA, USA from four plantings performed over 2 years and including two irrigation methods and inoculations with an attenuated strain of Escherichia coli O157:H7. High-throughput DNA pyrosequencing of the V5 to V9 variable regions of bacterial 16S rRNA genes recovered in lettuce leaf washes revealed that the bacterial diversity in the phyllosphere was distinct for each field trial but was also strongly correlated with the season of planting. Firmicutes were generally most abundant in early season (June) plantings and Proteobacteria comprised the majority of bacteria recovered later in the year (August and October). Comparisons within individual field trials showed that bacterial diversity differed between sprinkler (overhead) and drip (surface) irrigated lettuce and increased over time as the plants grew. The microbiota were also distinct between control and E. coli O157:H7-inoculated plants and between E. coli O157:H7-inoculated plants with and without surviving pathogen cells. The bacterial inhabitants of the phyllosphere therefore appear to be affected by seasonal, irrigation, and biological factors in ways that are relevant for assessments of fresh produce food safety. PMID:23844230

  6. Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes.

    Science.gov (United States)

    Lopez-Fernandez, Margarita; Cherkouk, Andrea; Vilchez-Vargas, Ramiro; Jauregui, Ruy; Pieper, Dietmar; Boon, Nico; Sanchez-Castro, Ivan; Merroun, Mohamed L

    2015-11-01

    The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work, the bacterial population of bentonite formations of Almeria (Spain), selected as a reference material for bentonite-engineered barriers in the disposal of radioactive wastes, was studied. 16S ribosomal RNA (rRNA) gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina sequencing. Using both techniques, the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria, Nitrospirae, Verrucomicrobia and an unknown phylum. The dominant groups of the community were represented by Proteobacteria and Bacteroidetes. A high diversity was found in three of the studied samples. However, two samples were less diverse and dominated by Betaproteobacteria.

  7. UV radiation and organic matter composition shape bacterial functional diversity in sediments

    Directory of Open Access Journals (Sweden)

    Ellard Roy Hunting

    2013-10-01

    Full Text Available AbstractUV radiation and organic matter (OM composition are known to influence the speciescomposition of bacterioplankton communities. Potential effects of UV radiation onbacterial communities residing in sediments remain completely unexplored to date.However, it has been demonstrated that UV radiation can reach the bottom of shallowwaters and wetlands and alter the OM composition of the sediment, suggesting thatUV radiation may be more important for sediment bacteria than previously anticipated.It is hypothesized here that exposure of shallow OMcontaining sediments to UVradiation induces OMsource dependant shifts in the functional composition ofsediment bacterial communities. This study therefore investigated the combinedinfluence of both UV radiation and OM composition on bacterial functional diversity inlaboratory sediments. Two different organic matter sources, labile and recalcitrantorganic matter (OM, were used and metabolic diversity was measured with BiologGN. Radiation exerted strong negative effects on the metabolic diversity in thetreatments containing recalcitrant OM, more than in treatments containing labile OM.The functional composition of the bacterial community also differed significantlybetween the treatments. Our findings demonstrate that a combined effect of UVradiation and OM composition shapes the functional composition of microbialcommunities developing in sediments, hinting that UV radiation may act as animportant sorting mechanism for bacterial communities and driver for bacterialfunctioning in shallow lakes and wetlands.

  8. Bacterial diversity in the sediment from polymetallic nodule fields of the Clarion-Clipperton Fracture Zone.

    Science.gov (United States)

    Wang, Chun-Sheng; Liao, Li; Xu, Hong-Xiang; Xu, Xue-Wei; Wu, Min; Zhu, Li-Zhong

    2010-10-01

    The Clarion-Clipperton Fracture Zone (CCFZ) is located in the northeastern equatorial Pacific and contains abundant polymetallic nodules. To investigate its bacterial diversity, four libraries of 16S rRNA genes were constructed from sediments of four stations in different areas of the CCFZ. In total, 313 clones sequenced from the 4 libraries were assigned into 14 phylogenetic groups and 1 group of 28 unclassified bacteria. High bacterial diversity was predicted by the rarefaction analysis. The most dominant group overall was Proteobacteria, but there was variation in each library: Gammaproteobacteria was the most dominant group in two libraries, E2005-01 and ES0502, while Alphaproteobacteria and Deltaproteobacteria were the most dominant groups in libraries EP2005-03 and WS0505, respectively. Seven groups, including Alphaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Betaproteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes, were common to all four libraries. The remaining minor groups were distributed in libraries with different patterns. Most clones sequenced in this study were clustered with uncultured bacteria obtained from the environment, such as the ocean crust and marine sediment, but only distantly related to isolates. Bacteria involved in the cycling of metals, sulfur and nitrogen were detected, and their relationship with their habitat was discussed. This study sheds light on the bacterial communities associated with polymetallic nodules in the CCFZ and provides primary data on the bacterial diversity of this area.

  9. Hydrogeochemical characteristics and bacterial community diversity in leachate from animal carcass disposal

    Science.gov (United States)

    Kaown, D.; Kim, H.; Lee, S.; Hyun, Y.; Moon, H.; Ko, K.; Lee, K.

    2012-12-01

    The release of leachate from animal carcass disposal can potentially contaminate soil and groundwater. During the Korea's foot-and-mouth disease (FMD) outbreak in 2010-2011, about 3.53 million of pigs and cattle were slaughtered and 4,538 burial sites were constructed. The objectives of this study are to determine the hydrogeochemical characteristics and bacterial community diversity in leachate from animal carcass disposal. Hydrogeochemical characteristics and bacterial community diversity in leachate from animal carcass burial facilities were monitored to prevent further soil and groundwater contamination and to build effective plans for stabilization of the burial site. Two burial sites were investigated in this study. An animal carcass disposal site is located in a flat area and another disposal site is found in mountain area. The hydrogeochemical and hydrogeological characteristics were analyzed to identify groundwater contamination by leachate from livestock burial sites. After 5-6 months of burial, the concentrations of NH4+, Cl-, and HCO3- in leachate were decreased since the leachate was regularly pumped and treated. However, high concentrations of major contaminants (NH4+, Cl-, and HCO3-) were still observed in landfill leachate of mountain area even though pumping and treatment of leachate were continuously conducted. Bacterial community diversity over time in leachate from animal carcass disposal was analyzed using 16S rRNA gene-based pyrosequencing. The impact of landfill leachate on change of bacterial community in soil and groundwater were monitored for a year.

  10. Functional diversity and redundancy across fish gut, sediment and water bacterial communities.

    Science.gov (United States)

    Escalas, Arthur; Troussellier, Marc; Yuan, Tong; Bouvier, Thierry; Bouvier, Corinne; Mouchet, Maud A; Flores Hernandez, Domingo; Ramos Miranda, Julia; Zhou, Jizhong; Mouillot, David

    2017-08-01

    This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (β) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  11. [Species diversity of ex-situ cultivated Chinese medicinal plants].

    Science.gov (United States)

    Que, Ling; Chi, Xiu-Lian; Zang, Chun-Xin; Zhang, Yu; Chen, Min; Yang, Guang; Jin, An-Qi

    2018-03-01

    Ex-situ conservation is an important means to protect biological genetic resources. Resource protection has received more and more attention with the continuous improvement of the comprehensive utilization of traditional Chinese medicine resources. In this paper, the research and compilation of the species list of ex-situ cultivated medicinal plants in 12 Chinese Academy of Sciences botanic gardens and 19 specialized medicinal botanic gardens in China were carried out. Based on the Species 2000(2017) and other classification databases, species diversity of medicinal plants ex-situ cultivated in these botanical gardens were analyzed. The study found that there were 16 351 higher plant species in our country, belonging to 276 families and 1 936 genera. Of these, 6 949 specieswere medicinal plants, accounting for 50.4% of the total medicinal plants. There were 1 280 medicinal plants were in threatened status, accounting for 19.6% of all threatened species in the Chinese Biodiversity Red List, with ex-situ cultivated proportion of 59.5%. And 3 988 medicinal plants were Chinese endemic species, accounting for 22.5% of all Chinese endemic species, with ex-situ cultivated proportion of 53.3%. This article has reference significance for the management and protection of medicinal plant resources. Copyright© by the Chinese Pharmaceutical Association.

  12. ‘Lachnoclostridium massiliosenegalense’, a new bacterial species isolated from the human gut microbiota

    Directory of Open Access Journals (Sweden)

    M. Tidjani Alou

    2016-11-01

    Full Text Available We report the main characteristics of ‘Lachnoclostridium massiliosenegalense’ strain mt23T (=CSUR P299 =DSM 102084, a new bacterial species isolated from the gut microbiota of a healthy young girl from Senegal.

  13. Both species sorting and neutral processes drive assembly of bacterial communities in aquatic microcosms

    NARCIS (Netherlands)

    Lee, Jack E.; Buckley, Hannah L.; Etienne, Rampal S.; Lear, Gavin

    2013-01-01

    A focus of ecology is to determine drivers of community assembly. Here, we investigate effects of immigration and species sorting (environmental selection) on structuring aquatic bacterial communities in both colonised and previously uncolonised environments. We used nonsterilised and presterilised

  14. Effect of Condensed Tannins on Bacterial Diversity and Metabolic Activity in the Rat Gastrointestinal Tract

    Science.gov (United States)

    Smith, Alexandra H.; Mackie, Roderick I.

    2004-01-01

    The effect of dietary condensed tannins (proanthocyanidins) on rat fecal bacterial populations was ascertained in order to determine whether the proportion on tannin-resistant bacteria increased and if there was a change in the predominant bacterial populations. After 3 weeks of tannin diets the proportion of tannin-resistant bacteria increased significantly (P tannin diet and to 47.2% ± 5.1% with a 2% tannin diet. The proportion of tannin-resistant bacteria returned to preexposure levels in the absence of dietary tannins. A shift in bacterial populations was confirmed by molecular fingerprinting of fecal bacterial populations by denaturing gradient gel electrophoresis (DGGE). Posttreatment samples were generally still distinguishable from controls after 3.5 weeks. Sequence analysis of DGGE bands and characterization of tannin-resistant isolates indicated that tannins selected for Enterobacteriaceae and Bacteroides species. Dot blot quantification confirmed that these gram-negative bacterial groups predominated in the presence of dietary tannins and that there was a corresponding decrease in the gram-positive Clostridium leptum group and other groups. Metabolic fingerprint patterns revealed that functional activities of culturable fecal bacteria were affected by the presence of tannins. Condensed tannins of Acacia angustissima altered fecal bacterial populations in the rat gastrointestinal tract, resulting in a shift in the predominant bacteria towards tannin-resistant gram-negative Enterobacteriaceae and Bacteroides species. PMID:14766594

  15. Diversity of endophytic fungal and bacterial communities in Ilex paraguariensis grown under field conditions.

    Science.gov (United States)

    Pérez, María Laura; Collavino, Mónica Mariana; Sansberro, Pedro Alfonso; Mroginski, Luis Amado; Galdeano, Ernestina

    2016-04-01

    The composition and diversity of the endophytic community associated with yerba mate (Ilex paraguariensis) was investigated using culture-depending methods. Fungi were identified based on their micromorphological characteristics and internal transcribed spacer rDNA sequence analysis; for bacteria 16S rDNA sequence analysis was used. Fungal and bacterial diversity did not show significant differences between organ age. The highest fungal diversity was registered during fall season and the lowest in winter. Bacterial diversity was higher in stems and increased from summer to winter, in contrast with leaves, which decreased. The most frequently isolated fungus was Fusarium, followed by Colletotrichum; they were both present in all the sampling seasons and organ types assayed. Actinobacteria represented 57.5 % of all bacterial isolates. The most dominant bacterial taxa were Curtobacterium and Microbacterium. Other bacteria frequently found were Methylobacterium, Sphingomonas, Herbiconiux and Bacillus. Nitrogen fixation and phosphate solubilization activity, ACC deaminase production and antagonism against plant fungal pathogens were assayed in endophytic bacterial strains. In the case of fungi, strains of Trichoderma, Penicillium and Aspergillus were assayed for antagonism against pathogenic Fusarium sp. All microbial isolates assayed showed at least one growth promoting activity. Strains of Bacillus, Pantoea, Curtobacterium, Methylobacterium, Brevundimonas and Paenibacillus had at least two growth-promoting activities, and Bacillus, Paenibacillus and the three endophytic fungi showed high antagonistic activity against Fusarium sp. In this work we have made a wide study of the culturable endophytic community within yerba mate plants and found that several microbial isolates could be considered as potential inoculants useful for improving yerba mate production.

  16. Covariation of viral parameters with bacterial assemblage richness and diversity in the water column and sediments

    Science.gov (United States)

    Hewson, Ian; Fuhrman, Jed A.

    2007-05-01

    Viruses are hypothesized to maintain diversity in microbial assemblages by regulating the abundance of dominant competitors and thereby allowing less-dominant competitors to persist in assemblages; however, there have been few empirical data sets to support this idea. In this study, we examined the relationship between the ratio of viral abundance to bacterial abundance, viral production, and the relative richness and diversity of bacterial assemblage fingerprints, in samples taken from geographically widespread locations (North Pacific gyre, the Amazon River plume and adjacent North Atlantic gyre, Gulf of Mexico, Southern California Bight and Arafura—Coral Seas) which are oligo- to mesotrophic. Bacterial assemblage richness and diversity as measured by automated rRNA intergenic spacer (ARISA) fingerprinting were significantly and positively correlated with the ratio of virus abundance to bacteria abundance (VBR) and to the rate of virus production only in the oligotrophic North Pacific gyre. ARISA fingerprint richness/diversity were not significantly correlated to viral parameters when assessed across all samples in surface waters, suggesting there is not a singular global quantitative relationship between viral pressure and host diversity within well evolved host/virus systems in different geographic locations in plankton. In sediments off Southern California, viral parameters significantly and negatively correlated with ARISA diversity, suggesting strong viral interactions in this habitat. To examine covariation of viral parameters and the relative abundance and diversity of rarer bacterial taxa (i.e., less-dominant competitor), the richness and diversity of diazotroph communities was measured using terminal restriction fragment length polymorphism (TRFLP) of a portion ( nifH) of the nitrogenase gene. The richness and diversity of diazotrophic communities were significantly and negatively correlated with viral parameters across all locations. Since diazotrophs

  17. Bacterial community diversity and variation in spray water sources and the tomato fruit surface.

    Science.gov (United States)

    Telias, Adriana; White, James R; Pahl, Donna M; Ottesen, Andrea R; Walsh, Christopher S

    2011-04-21

    Tomato (Solanum lycopersicum) consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water) when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production. The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant. Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an important step forward towards the development of science

  18. Bacterial community diversity and variation in spray water sources and the tomato fruit surface

    Directory of Open Access Journals (Sweden)

    Ottesen Andrea R

    2011-04-01

    Full Text Available Abstract Background Tomato (Solanum lycopersicum consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production. Results The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant. Conclusions Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an

  19. Microbial Ecophysiology of Whey Biomethanation: Characterization of Bacterial Trophic Populations and Prevalent Species in Continuous Culture

    OpenAIRE

    Chartrain, M.; Zeikus, J. G.

    1986-01-01

    The organization and species composition of bacterial trophic groups associated with lactose biomethanation were investigated in a whey-processing chemostat by enumeration, isolation, and general characterization studies. The bacteria were spatially organized as free-living forms and as self-immobilized forms appearing in flocs. Three dominant bacterial trophic group populations were present (in most probable number per milliliter) whose species numbers varied with the substrate consumed: hyd...

  20. Bacterial diversity in relatively pristine and anthropogenically-influenced mangrove ecosystems (Goa, India

    Directory of Open Access Journals (Sweden)

    Sheryl Oliveira Fernandes

    2014-12-01

    Full Text Available To appreciate differences in benthic bacterial community composition at the relatively pristine Tuvem and the anthropogenically-influenced Divar mangrove ecosystems in Goa, India, parallel tag sequencing of the V6 region of 16S rDNA was carried out. We hypothesize that availability of extraneously-derived anthropogenic substrates could act as a stimulatant but not a deterrent to promote higher bacterial diversity at Divar. Our observations revealed that the phylum Proteobacteria was dominant at both locations comprising 43-46% of total tags. The Tuvem ecosystem was characterized by an abundance of members belonging to the class Deltaproteobacteria (21%, ~ 2100 phylotypes and 1561 operational taxonomic units (OTUs sharing > 97% similarity. At Divar, the Gammaproteobacteria were ~ 2x higher (17% than at Tuvem. A more diverse bacterial community with > 3300 phylotypes and > 2000 OTUs mostly belonging to Gammaproteobacteria and a significantly higher DNT (n = 9, p < 0.001, df = 1 were recorded at Divar. These findings suggest that the quantity and quality of pollutants at Divar are perhaps still at a level to maintain high diversity. Using this technique we could show higher diversity at Divar with the possibility of Gammaproteobacteria contributing to modulating excess nitrate.

  1. Parallel responses of species and genetic diversity to El Nino Southern Oscillation-induced environmental destruction

    NARCIS (Netherlands)

    Cleary, D.F.R.; Fauvelot, C.Y.; Genner, J.; Menken, S.B.J.; Mooers, A.O.

    2006-01-01

    Species diversity within communities and genetic diversity within species are two fundamental levels of biodiversity. Positive relationships between species richness and within-species genetic diversity have recently been documented across natural and semi-natural habitat islands, leading Vellend to

  2. Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China

    Directory of Open Access Journals (Sweden)

    Yucheng eWu

    2015-03-01

    Full Text Available Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit (SSU rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the -Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments.

  3. Distribution and diversity of twelve Curcuma species in China.

    Science.gov (United States)

    Zhang, Lanyue; Wei, Jingwen; Yang, Zhiwen; Chen, Feng; Xian, Qiqiu; Su, Ping; Pan, Wanyi; Zhang, Kun; Zheng, Xi; Du, Zhiyun

    2018-02-01

    Genus Curcuma a wild species presents an important source of valuable characters for improving the cultivated Curcuma varieties. Based on the collected germplasms, herbariums, field surveys and other literatures, the ecogeographical diversity of Genus Curcuma and its potential distributions under the present and future climate are analysed by DIVA-GIS. The results indicate Genus Curcuma is distributed over 17 provinces in China, and particularly abundant in Guangxi and Guangdong provinces. The simulated current distributions are close to the actual distribution regions. In the future climate, the suitable areas for four Curcuma species will be extended, while for other three species the regions will be significantly decreased, and thus these valuable resources need protecting.

  4. Differences in bacterial diversity of host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory.

    Science.gov (United States)

    Medina, R F; Nachappa, P; Tamborindeguy, C

    2011-04-01

    Host-associated differentiation (HAD) is the presence of genetically divergent, host-associated populations. It has been suggested that microbial symbionts of insect herbivores may play a role in HAD by allowing their insect hosts to use different plant species. The objective of this study was to document if host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory corresponded with differences in the composition of their associated bacteria. To test this hypothesis, we characterized the symbionts present in P. notabilis associated with these two tree species through metagenomic analyses using 454 sequencing. Differences in bacterial diversity were found between P. notabilis populations associated with pecan and water hickory. The bacteria, Pantoea agglomerans and Serratia marcescens, were absent in the P. notabilis water hickory population, whereas both species accounted for more than 69.72% of bacterial abundance in the pecan population. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  5. Diversity of small RNAs expressed in Pseudomonas species

    DEFF Research Database (Denmark)

    Gomez-Lozano, Mara; Marvig, Rasmus Lykke; Molina-Santiago, Carlos

    2015-01-01

    RNA sequencing (RNA-seq) has revealed several hundreds of previously undetected small RNAs (sRNAs) in all bacterial species investigated, including strains of Pseudomonas aeruginosa, Pseudomonas putida and Pseudomonas syringae. Nonetheless, only little is known about the extent of conservation...... of expressed sRNAs across strains and species. In this study, we have used RNA-seq to identify sRNAs in P.putidaDOT-T1E and Pseudomonas extremaustralis 14-3b. This is the first strain of P.extremaustralis and the second strain of P.putida to have their transcriptomes analysed for sRNAs, and we identify...... the presence of around 150 novel sRNAs in each strain. Furthermore, we provide a comparison based on sequence conservation of all the sRNAs detected by RNA-seq in the Pseudomonas species investigated so far. Our results show that the extent of sRNA conservation across different species is very limited...

  6. Confocal Raman microscopy for identification of bacterial species in biofilms

    Science.gov (United States)

    Beier, Brooke D.; Quivey, Robert G.; Berger, Andrew J.

    2011-03-01

    Implemented through a confocal microscope, Raman spectroscopy has been used to distinguish between biofilm samples of two common oral bacteria species, Streptococcus sanguinis and mutans, which are associated with healthy and cariogenic plaque, respectively. Biofilms of these species are studied as a model of dental plaque. A prediction model has been calibrated and validated using pure biofilms. This model has been used to identify the species of transferred and dehydrated samples (much like a plaque scraping) as well as hydrated biofilms in situ. Preliminary results of confocal Raman mapping of species in an intact two-species biofilm will be shown.

  7. Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

    Directory of Open Access Journals (Sweden)

    Xiaorui Chen

    2017-10-01

    Full Text Available Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle.

  8. Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

    Science.gov (United States)

    Chen, Xiaorui; Hitchings, Matthew D.; Mendoza, José E.; Balanza, Virginia; Facey, Paul D.; Dyson, Paul J.; Bielza, Pablo; Del Sol, Ricardo

    2017-01-01

    Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis) from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle. PMID:29067021

  9. Factors shaping bacterial phylogenetic and functional diversity in coastal waters of the NW Mediterranean Sea

    Science.gov (United States)

    Boras, Julia A.; Vaqué, Dolors; Maynou, Francesc; Sà, Elisabet L.; Weinbauer, Markus G.; Sala, Maria Montserrat

    2015-03-01

    To evaluate the main factors shaping bacterioplankton phylogenetic and functional diversity in marine coastal waters, we carried out a two-year study based on a monthly sampling in Blanes Bay (NW Mediterranean). We expected the key factors driving bacterial diversity to be (1) temperature and nutrient concentration, together with chlorophyll a concentration as an indicator of phytoplankton biomass and, hence, a carbon source for bacteria (here called bottom-up factors), and (2) top-down pressure (virus- and protist-mediated mortality of bacteria). Phylogenetic diversity was analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA. Functional diversity was assessed by using monomeric carbon sources in Biolog EcoPlates and by determining the activity of six extracellular enzymes. Our results indicate that the bacterial phylogenetic and functional diversity in this coastal system is shaped mainly by bottom-up factors. A dendrogram analysis of the DGGE banding patterns revealed three main sample clusters. Two clusters differed significantly in temperature, nitrate and chlorophyll a concentration, and the third was characterized by the highest losses of bacterial production due to viral lysis detected over the whole study period. Protistan grazing had no effect on bacterial functional diversity, since there were no correlations between protist-mediated mortality (PMM) and extracellular enzyme activities, and utilization of only two out of the 31 carbon sources (N-acetyl-D-glucosamine and α-cyclodextrin) was correlated with PMM. In contrast, virus-mediated mortality correlated with changes in the percentage of use of four carbon sources, and also with specific leu-aminopeptidase and β-glucosidase activity. This suggests that viral lysate provides a pool of labile carbon sources, presumably including amino acids and glucose, which may inhibit proteolytic and glucosidic activity. Our results indicate that bottom-up factors play a more important role than

  10. UV radiation and organic matter composition shape bacterial functional diversity in sediments

    NARCIS (Netherlands)

    Hunting, E.R.; White, C.M.; van Gemert, M.; Mes, D.; Stam, E.; van der Geest, H.G.; Kraak, M.H.S.; Admiraal, W.

    2013-01-01

    UV radiation and organic matter (OM) composition are known to influence the species composition of bacterioplankton communities. Potential effects of UV radiation on bacterial communities residing in sediments remain completely unexplored to date. However, it has been demonstrated that UV radiation

  11. Marine diversity: the paradigms in patterns of species richness examined

    Directory of Open Access Journals (Sweden)

    John S. Gray

    2001-12-01

    Full Text Available The two central paradigms of marine diversity are that there is a latitudinal cline of increasing species richness from poles to tropics and that species richness increases with depth to a maximum around 2,000 m and thereafter decreases. However, these paradigms were based on data collected in the late 1950´s and early 1960´s. Here I show that the 1960´s data, are not representative and thus the paradigms need re-examination. New data from coastal areas in the northern hemisphere record species richness as high as the highest recorded in the deep-sea. Whilst this suggests that the cline of increasing diversity from shallow to deep-sea does not exist, however, the database for the deep sea is not sufficient to draw such a conclusion. The basic problem with the data from the 1960s is that samples were taken on ecological scales and yet they are used to answer evolutionary questions. The questions that such data were to answer were why do the tropics have higher species richness than polar regions or why do deep-sea sediments have more species than coastal sediments? Evolutionary questions need data from much larger spatial areas. Recently, data representative of large scales have been collected from coastal areas in the northern hemisphere and show that there is a cline of increasing species richness from the Arctic to the tropics, but there does not yet seem to be a similar cline in the southern hemisphere. A number of hypotheses have been proposed for the observed patterns in biodiversity. In terrestrial ecology the energy-productivity hypothesis has gained wide acceptance as an explanation for the latitudinal gradient. Here I examine this and other hypotheses critically. Finally an analysis of research priorities is made. Assessment is urgently needed of the spatial scales and dynamics of species richness from point samples to assemblages, habitats and landscapes, especially in coastal areas and in the tropics, where the threats to

  12. Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches

    Directory of Open Access Journals (Sweden)

    Delavat François

    2012-09-01

    Full Text Available Abstract Background Acid Mine Drainages (AMDs are extreme environments characterized by very acid conditions and heavy metal contaminations. In these ecosystems, the bacterial diversity is considered to be low. Previous culture-independent approaches performed in the AMD of Carnoulès (France confirmed this low species richness. However, very little is known about the cultured bacteria in this ecosystem. The aims of the study were firstly to apply novel culture methods in order to access to the largest cultured bacterial diversity, and secondly to better define the robustness of the community for 3 important functions: As(III oxidation, cellulose degradation and cobalamine biosynthesis. Results Despite the oligotrophic and acidic conditions found in AMDs, the newly designed media covered a large range of nutrient concentrations and a pH range from 3.5 to 9.8, in order to target also non-acidophilic bacteria. These approaches generated 49 isolates representing 19 genera belonging to 4 different phyla. Importantly, overall diversity gained 16 extra genera never detected in Carnoulès. Among the 19 genera, 3 were previously uncultured, one of them being novel in databases. This strategy increased the overall diversity in the Carnoulès sediment by 70% when compared with previous culture-independent approaches, as specific phylogenetic groups (e.g. the subclass Actinobacteridae or the order Rhizobiales were only detected by culture. Cobalamin auxotrophy, cellulose degradation and As(III-oxidation are 3 crucial functions in this ecosystem, and a previous meta- and proteo-genomic work attributed each function to only one taxon. Here, we demonstrate that other members of this community can also assume these functions, thus increasing the overall community robustness. Conclusions This work highlights that bacterial diversity in AMDs is much higher than previously envisaged, thus pointing out that the AMD system is functionally more robust than expected

  13. Bacterial diversity in Greenlandic soils as affected by potato cropping and inorganic versus organic fertilization

    DEFF Research Database (Denmark)

    Michelsen, Charlotte Frydenlund; Pedas, Pai Rosager; Glaring, Mikkel Andreas

    2014-01-01

    research has been performed on the effects of these treatments on bacterial communities in Arctic and Subarctic agricultural soils. The major objective of this study was to investigate the short-term impact of conventional (NPK) and organic (sheep manure supplemented with nitrogen) fertilizer treatments...... with only limited pest management, despite the presence of plant pathogenic fungi. The microbial community composition in agricultural soils, which plays an important role for soil and plant health and for crop yield, may be affected by the use of different fertilizer treatments. Currently, only limited...... on bacterial diversity, nutrient composition and crop yield in two Greenlandic agricultural soils. An effect of fertilizer was found on soil and plant nutrient levels and on crop yields. Pyrosequencing of 16S rRNA gene sequences did not reveal any major changes in the overall bacterial community composition...

  14. Bacterial diversity and biogeography in deep-sea sediments of the South Atlantic Ocean

    DEFF Research Database (Denmark)

    Schauer, Regina; Bienhold, Christina; Ramette, Alban

    2010-01-01

    in 1051 sequences. Phylotypes affiliated with Gammaproteobacteria, Deltaproteobacteria and Acidobacteria were present in all three basins. The distribution of these shared phylotypes seemed to be influenced neither by the Walvis Ridge nor by different deep water masses, suggesting a high dispersal......Microbial biogeographic patterns in the deep sea depend on the ability of microorganisms to disperse. One possible limitation to microbial dispersal may be the Walvis Ridge that separates the Antarctic Lower Circumpolar Deep Water from the North Atlantic Deep Water. We examined bacterial...... communities in three basins of the eastern South Atlantic Ocean to determine diversity and biogeography of bacterial communities in deep-sea surface sediments. The analysis of 16S ribosomal RNA (rRNA) gene clone libraries in each basin revealed a high diversity, representing 521 phylotypes with 98% identity...

  15. Characterization of bacterial diversity in pulque, a traditional Mexican alcoholic fermented beverage, as determined by 16S rDNA analysis.

    Science.gov (United States)

    Escalante, Adelfo; Rodríguez, María Elena; Martínez, Alfredo; López-Munguía, Agustín; Bolívar, Francisco; Gosset, Guillermo

    2004-06-15

    The bacterial diversity in pulque, a traditional Mexican alcoholic fermented beverage, was studied in 16S rDNA clone libraries from three pulque samples. Sequenced clones identified as Lactobacillus acidophilus, Lactobacillus strain ASF360, L. kefir, L. acetotolerans, L. hilgardii, L. plantarum, Leuconostoc pseudomesenteroides, Microbacterium arborescens, Flavobacterium johnsoniae, Acetobacter pomorium, Gluconobacter oxydans, and Hafnia alvei, were detected for the first time in pulque. Identity of 16S rDNA sequenced clones showed that bacterial diversity present among pulque samples is dominated by Lactobacillus species (80.97%). Seventy-eight clones exhibited less than 95% of relatedness to NCBI database sequences, which may indicate the presence of new species in pulque samples.

  16. Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes.

    Directory of Open Access Journals (Sweden)

    Luka Ausec

    Full Text Available Fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. Although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within Bacteria. In this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and four metagenomic datasets, using the custom profile Hidden Markov Models for two- and three-domain laccases. More than 1,200 putative genes for laccase-like enzymes were retrieved from chromosomes and plasmids of diverse bacteria. In 76% of the genes, signal peptides were predicted, indicating that these bacterial laccases may be exported from the cytoplasm, which contrasts with the current belief. Moreover, several examples of putatively horizontally transferred bacterial laccase genes were described. Many metagenomic sequences encoding fragments of laccase-like enzymes could not be phylogenetically assigned, indicating considerable novelty. Laccase-like genes were also found in anaerobic bacteria, autotrophs and alkaliphiles, thus opening new hypotheses regarding their ecological functions. Bacteria identified as carrying laccase genes represent potential sources for future biotechnological applications.

  17. Bacterial diversity of surface sand samples from the Gobi and Taklamaken deserts.

    Science.gov (United States)

    An, Shu; Couteau, Cécile; Luo, Fan; Neveu, Julie; DuBow, Michael S

    2013-11-01

    Arid regions represent nearly 30 % of the Earth's terrestrial surface, but their microbial biodiversity is not yet well characterized. The surface sands of deserts, a subset of arid regions, are generally subjected to large temperature fluctuations plus high UV light exposure and are low in organic matter. We examined surface sand samples from the Taklamaken (China, three samples) and Gobi (Mongolia, two samples) deserts, using pyrosequencing of PCR-amplified 16S V1/V2 rDNA sequences from total extracted DNA in order to gain an assessment of the bacterial population diversity. In total, 4,088 OTUs (using ≥97 % sequence similarity levels), with Chao1 estimates varying from 1,172 to 2,425 OTUs per sample, were discernable. These could be grouped into 102 families belonging to 15 phyla, with OTUs belonging to the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria phyla being the most abundant. The bacterial population composition was statistically different among the samples, though members from 30 genera were found to be common among the five samples. An increase in phylotype numbers with increasing C/N ratio was noted, suggesting a possible role in the bacterial richness of these desert sand environments. Our results imply an unexpectedly large bacterial diversity residing in the harsh environment of these two Asian deserts, worthy of further investigation.

  18. Genetic diversity of Bromeliaceae species from the Atlantic Forest.

    Science.gov (United States)

    Sheu, Y; Cunha-Machado, A S; Gontijo, A B P L; Favoreto, F C; Soares, T B C; Miranda, F D

    2017-04-20

    The Bromeliaceae family includes a range of species used for many purposes, including ornamental use and use as food, medicine, feed, and fiber. The state of Espírito Santo, Brazil is a center of diversity for this family in the Atlantic Forest. We evaluated the genetic diversity of five populations of the Bromeliaceae family, including specimens of the genera Aechmea, Billbergia (subfamily Bromelioideae), and Pitcairnia (subfamily Pitcairnioidea), all found in the Atlantic Forest and distributed in the state of Espírito Santo. The number of alleles per locus in populations ranged from two to six and the fixation index (F), estimated for some simple sequence repeats in bromeliad populations, was less than zero in all populations. All markers in the Pitcairnia flammea population were in Hardy-Weinberg equilibrium (P Atlantic Forest remnants in the south of Espírito Santo state.

  19. Bacterial Diversity in Submarine Groundwater along the Coasts of the Yellow Sea

    OpenAIRE

    Ye, Qi; Liu, Jianan; Du, Jinzhou; Zhang, Jing

    2016-01-01

    Submarine groundwater (SGD) is one of the most significant pathways for the exchange of groundwater and/or source of nutrients, metals and carbon to the ocean, subsequently cause deleterious impacts on the coastal ecosystems. Microorganisms have been recognized as the important participators in the biogeochemical processes in the SGD. In this study, by utilizing 16S rRNA-based Illumina Miseq sequencing technology, we investigated bacterial diversity and distribution in both fresh well water a...

  20. Exploring bacterial diversity in hospital environments by GS-FLX Titanium pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Margarita Poza

    Full Text Available Understanding microbial populations in hospital environments is crucial for improving human health. Hospital-acquired infections are an increasing problem in intensive care units (ICU. In this work we present an exploration of bacterial diversity at inanimate surfaces of the ICU wards of the University Hospital A Coruña (Spain, as an example of confined hospital environment subjected to selective pressure, taking the entrance hall of the hospital, an open and crowded environment, as reference. Surface swab samples were collected from both locations and recovered DNA used as template to amplify a hypervariable region of the bacterial 16S rRNA gene. Sequencing of the amplicons was performed at the Roche 454 Sequencing Center using GS-FLX Titanium procedures. Reads were pre-processed and clustered into OTUs (operational taxonomic units, which were further classified. A total of 16 canonical bacterial phyla were detected in both locations. Members of the phyla Firmicutes (mainly Staphylococcus and Streptococcus and Actinobacteria (mainly Micrococcaceae, Corynebacteriaceae and Brevibacteriaceae were over-represented in the ICU with respect to the Hall. The phyllum Proteobacteria was also well represented in the ICU, mainly by members of the families Enterobacteriaceae, Methylobacteriaceae and Sphingomonadaceae. In the Hall sample, the phyla Proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria were over-represented with respect to the ICU. Over-representation of Proteobacteria was mainly due to the high abundance of Enterobacteriaceae members. The presented results demonstrate that bacterial diversity differs at the ICU and entrance hall locations. Reduced diversity detected at ICU, relative to the entrance hall, can be explained by its confined character and by the existence of antimicrobial selective pressure. This is the first study using deep sequencing techniques made in hospital wards showing substantial hospital microbial

  1. Exploring bacterial diversity in hospital environments by GS-FLX Titanium pyrosequencing.

    Science.gov (United States)

    Poza, Margarita; Gayoso, Carmen; Gómez, Manuel J; Rumbo-Feal, Soraya; Tomás, María; Aranda, Jesús; Fernández, Ana; Bou, Germán

    2012-01-01

    Understanding microbial populations in hospital environments is crucial for improving human health. Hospital-acquired infections are an increasing problem in intensive care units (ICU). In this work we present an exploration of bacterial diversity at inanimate surfaces of the ICU wards of the University Hospital A Coruña (Spain), as an example of confined hospital environment subjected to selective pressure, taking the entrance hall of the hospital, an open and crowded environment, as reference. Surface swab samples were collected from both locations and recovered DNA used as template to amplify a hypervariable region of the bacterial 16S rRNA gene. Sequencing of the amplicons was performed at the Roche 454 Sequencing Center using GS-FLX Titanium procedures. Reads were pre-processed and clustered into OTUs (operational taxonomic units), which were further classified. A total of 16 canonical bacterial phyla were detected in both locations. Members of the phyla Firmicutes (mainly Staphylococcus and Streptococcus) and Actinobacteria (mainly Micrococcaceae, Corynebacteriaceae and Brevibacteriaceae) were over-represented in the ICU with respect to the Hall. The phyllum Proteobacteria was also well represented in the ICU, mainly by members of the families Enterobacteriaceae, Methylobacteriaceae and Sphingomonadaceae. In the Hall sample, the phyla Proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria were over-represented with respect to the ICU. Over-representation of Proteobacteria was mainly due to the high abundance of Enterobacteriaceae members. The presented results demonstrate that bacterial diversity differs at the ICU and entrance hall locations. Reduced diversity detected at ICU, relative to the entrance hall, can be explained by its confined character and by the existence of antimicrobial selective pressure. This is the first study using deep sequencing techniques made in hospital wards showing substantial hospital microbial diversity.

  2. Exploring Bacterial Diversity in Hospital Environments by GS-FLX Titanium Pyrosequencing

    OpenAIRE

    Poza, Margarita; Gayoso, Carmen; Gómez, Manuel J.; Rumbo-Feal, Soraya; Tomás, María; Aranda, Jesús; Fernández, Ana; Bou, Germán

    2012-01-01

    Understanding microbial populations in hospital environments is crucial for improving human health. Hospital-acquired infections are an increasing problem in intensive care units (ICU). In this work we present an exploration of bacterial diversity at inanimate surfaces of the ICU wards of the University Hospital A Coruña (Spain), as an example of confined hospital environment subjected to selective pressure, taking the entrance hall of the hospital, an open and crowded environment, as referen...

  3. Species diversity of culturable endophytic fungi from Brazilian mangrove forests.

    Science.gov (United States)

    de Souza Sebastianes, Fernanda Luiza; Romão-Dumaresq, Aline Silva; Lacava, Paulo Teixeira; Harakava, Ricardo; Azevedo, João Lúcio; de Melo, Itamar Soares; Pizzirani-Kleiner, Aline Aparecida

    2013-08-01

    This study aimed to perform a comparative analysis of the diversity of endophytic fungal communities isolated from the leaves and branches of Rhizophora mangle, Avicennia schaueriana and Laguncularia racemosa trees inhabiting two mangroves in the state of São Paulo, Brazil [Cananeia and Bertioga (oil spill-affected and unaffected)] in the summer and winter. Three hundred and forty-three fungi were identified by sequencing the ITS1-5.8S-ITS2 region of rDNA. Differences were observed in the frequencies of fungi isolated from the leaves and branches of these three different plant species sampled from the Bertioga oil spill-affected and the oil-unaffected mangrove sites in the summer and winter; these differences indicate a potential impact on fungal diversity in the study area due to the oil spill. The molecular identification of the fungi showed that the fungal community associated with these mangroves is composed of at least 34 different genera, the most frequent of which were Diaporthe, Colletotrichum, Fusarium, Trichoderma and Xylaria. The Shannon and the Chao1 indices [H'(95 %) = 4.00, H'(97 %) = 4.22, Chao1(95 %) = 204 and Chao1(97 %) = 603] indicated that the mangrove fungal community possesses a vast diversity and richness of endophytic fungi. The data generated in this study revealed a large reservoir of fungal genetic diversity inhabiting these Brazilian mangrove forests and highlighted substantial differences between the fungal communities associated with distinct plant tissues, plant species, impacted sites and sampling seasons.

  4. In-depth diversity analysis of the bacterial community resident in the camel rumen.

    Science.gov (United States)

    Gharechahi, Javad; Zahiri, Hossein Shahbani; Noghabi, Kambiz Akbari; Salekdeh, Ghasem Hosseini

    2015-02-01

    The rumen compartment of the ruminant digestive tract is an enlarged fermentation chamber which houses a diverse collection of symbiotic microorganisms that provide the host animal with a remarkable ability to digest plant lignocellulosic materials. Characterization of the ruminal microbial community provides opportunities to improve animal food digestion efficiency, mitigate methane emission, and develop efficient fermentation systems to convert plant biomasses into biofuels. In this study, 16S rRNA gene amplicon pyrosequencing was applied in order to explore the structure of the bacterial community inhabiting the camel rumen. Using 76,333 quality-checked, chimera- and singleton-filtered reads, 4954 operational taxonomic units (OTUs) were identified at a 97% species level sequence identity. At the phylum level, more than 96% of the reads were affiliated to OTUs belonging to Bacteroidetes (51%), Firmicutes (31%), Proteobacteria (4.8%), Spirochaetes (3.5%), Fibrobacteres (3.1%), Verrucomicrobia (2.7%), and Tenericutes (0.95%). A total of 15% of the OTUs (746) that contained representative sequences from all major taxa were shared by all animals and they were considered as candidate members of the core camel rumen microbiome. Analysis of microbial composition through the solid and liquid fractions of rumen digesta revealed differential enrichment of members of Fibrobacter, Clostridium, Ruminococcus, and Treponema in the solid fraction, as well as members of Prevotella, Verrucomicrobia, Cyanobacteria, and Succinivibrio in the liquid fraction. The results clearly showed that the camel rumen microbiome was structurally similar but compositionally distinct from that of other ruminants, such as the cow. The unique characteristic of the camel rumen microbiome that differentiated it from those of other ruminants was the significant enrichment for cellulolytic bacteria. Copyright © 2014. Published by Elsevier GmbH.

  5. Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers.

    Science.gov (United States)

    Llewellyn, Anna C; Lucas, Claressa E; Roberts, Sarah E; Brown, Ellen W; Nayak, Bina S; Raphael, Brian H; Winchell, Jonas M

    2017-01-01

    Cooling towers (CTs) are a leading source of outbreaks of Legionnaires' disease (LD), a severe form of pneumonia caused by inhalation of aerosols containing Legionella bacteria. Accordingly, proper maintenance of CTs is vital for the prevention of LD. The aim of this study was to determine the distribution of Legionella in a subset of regionally diverse US CTs and characterize the associated microbial communities. Between July and September of 2016, we obtained aliquots from water samples collected for routine Legionella testing from 196 CTs located in eight of the nine continental US climate regions. After screening for Legionella by PCR, positive samples were cultured and the resulting Legionella isolates were further characterized. Overall, 84% (164) were PCR-positive, including samples from every region studied. Of the PCR-positive samples, Legionella spp were isolated from 47% (78), L. pneumophila was isolated from 32% (53), and L. pneumophila serogroup 1 (Lp1) was isolated from 24% (40). Overall, 144 unique Legionella isolates were identified; 53% (76) of these were Legionella pneumophila. Of the 76 L. pneumophila isolates, 51% (39) were Lp1. Legionella were isolated from CTs in seven of the eight US regions examined. 16S rRNA amplicon sequencing was used to compare the bacterial communities of CT waters with and without detectable Legionella as well as the microbiomes of waters from different climate regions. Interestingly, the microbial communities were homogenous across climate regions. When a subset of seven CTs sampled in April and July were compared, there was no association with changes in corresponding CT microbiomes over time in the samples that became culture-positive for Legionella. Legionella species and Lp1 were detected frequently among the samples examined in this first large-scale study of Legionella in US CTs. Our findings highlight that, under the right conditions, there is the potential for CT-related LD outbreaks to occur throughout the US.

  6. Antimicrobial effect of probiotics on bacterial species from dental plaque.

    Science.gov (United States)

    Zambori, Csilla; Morvay, Attila Alexandru; Sala, Claudia; Licker, Monica; Gurban, Camelia; Tanasie, Gabriela; Tirziu, Emil

    2016-03-31

    The antimicrobial role of probiotic Lactobacillus casei subspecies casei DG (L. casei DG) and of the mix culture of probiotic Lactobacillus acidophilus LA-5 and Bifidobacterium BB-12 was tested on species of Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera from supragingival sites from dogs with dental disease of different breed, age, sex, weight, and diet. The research was conducted on these four genera because of their importance in zoonotic infections after dog bites. Species from Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera were isolated and identified. To test the antimicrobial efficacy of L. casei DG and the mixed culture of probiotic L. acidophilus LA-5 and Bifidobacterium bifidum BB-12 on the pathogenic species, the agar overlay method was used. L. casei DG had a bactericidal effect on all analyzed species isolated from Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera after 24 hours of incubation. The mixed probiotic culture made up of L. acidophilus LA-5 and Bifidobacterium BB-12 species had no bactericidal effect on the species of Staphylococcus and Streptococcus genera, which were resistant. However, it had a bacteriostatic effect on several species of Pasteurella and Neisseria genera. This work highlights the antimicrobial potential of probiotics in vitro, demonstrating that the probiotic L. casei DG has a bactericidal effect on all analyzed species isolated from dental plaque and that the mix culture of probiotic L. acidophilus LA-5 and Bifidobacterium BB-12 has only a bacteriostatic effect.

  7. Changes of bacterial diversity and tetracycline resistance in sludge from AAO systems upon exposure to tetracycline pressure

    International Nuclear Information System (INIS)

    Huang, Manhong; Qi, Fangfang; Wang, Jue; Xu, Qi; Lin, Li

    2015-01-01

    Highlights: • High-throughput sequencing was used to compare sludge bacteria with and without TC. • Bacterial diversity increased with TC addition despite of various oxygen conditions. • Total TRGs proliferated with TC addition in three kinds of sludge. • The concentration of efflux pump genes was the highest in the three groups of TRGs. - Abstract: Two lab-scale anaerobic-anoxic-oxic (AAO) systems were used to investigate the changes in tetracycline (TC) resistance and bacterial diversity upon exposure to TC pressure. High-throughput sequencing was used to detect diversity changes in microorganisms at the level of class in sludge from different bioreactors with and without TC. Real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) was used to detect the abundances of eight tetracycline resistance genes (TRGs), tetA, tetB, tetC, tetE, tetM, tetO, tetS and tetX. The results showed that the diversities of the microbial communities of anoxic, anaerobic and aerobic sludge all increased with the addition of TC. TC substantially changed the structure of the microbial community regardless of oxygen conditions. Bacteroidetes and Proteobacteria were the dominant species in the three kinds of sludge and were substantially enriched with TC pressure. In sludge with TC added, almost all target TRGs proliferated more than those in sludge without TC except tetX, which decreased in anaerobic sludge with TC addition. The concentration of efflux pump genes, tet(A–C, E), was the highest among the three groups of TRGs in the different kinds of sludge

  8. Changes of bacterial diversity and tetracycline resistance in sludge from AAO systems upon exposure to tetracycline pressure

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Manhong, E-mail: egghmh@163.com; Qi, Fangfang; Wang, Jue; Xu, Qi; Lin, Li

    2015-11-15

    Highlights: • High-throughput sequencing was used to compare sludge bacteria with and without TC. • Bacterial diversity increased with TC addition despite of various oxygen conditions. • Total TRGs proliferated with TC addition in three kinds of sludge. • The concentration of efflux pump genes was the highest in the three groups of TRGs. - Abstract: Two lab-scale anaerobic-anoxic-oxic (AAO) systems were used to investigate the changes in tetracycline (TC) resistance and bacterial diversity upon exposure to TC pressure. High-throughput sequencing was used to detect diversity changes in microorganisms at the level of class in sludge from different bioreactors with and without TC. Real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) was used to detect the abundances of eight tetracycline resistance genes (TRGs), tetA, tetB, tetC, tetE, tetM, tetO, tetS and tetX. The results showed that the diversities of the microbial communities of anoxic, anaerobic and aerobic sludge all increased with the addition of TC. TC substantially changed the structure of the microbial community regardless of oxygen conditions. Bacteroidetes and Proteobacteria were the dominant species in the three kinds of sludge and were substantially enriched with TC pressure. In sludge with TC added, almost all target TRGs proliferated more than those in sludge without TC except tetX, which decreased in anaerobic sludge with TC addition. The concentration of efflux pump genes, tet(A–C, E), was the highest among the three groups of TRGs in the different kinds of sludge.

  9. Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China.

    Science.gov (United States)

    Song, Zhao-Qi; Wang, Feng-Ping; Zhi, Xiao-Yang; Chen, Jin-Quan; Zhou, En-Min; Liang, Feng; Xiao, Xiang; Tang, Shu-Kun; Jiang, Hong-Chen; Zhang, Chuanlun L; Dong, Hailiang; Li, Wen-Jun

    2013-04-01

    Thousands of hot springs are located in the north-eastern part of the Yunnan-Tibet geothermal zone, which is one of the most active geothermal areas in the world. However, a comprehensive and detailed understanding of microbial diversity in these hot springs is still lacking. In this study, bacterial and archaeal diversities were investigated in 16 hot springs (pH 3.2-8.6; temperature 47-96°C) in Yunnan Province and Tibet, China by using a barcoded 16S rRNA gene-pyrosequencing approach. Aquificae, Proteobacteria, Firmicutes, Deinococcus-Thermus and Bacteroidetes comprised the large portion of the bacterial communities in acidic hot springs. Non-acidic hot springs harboured more and variable bacterial phyla than acidic springs. Desulfurococcales and unclassified Crenarchaeota were the dominated groups in archaeal populations from most of the non-acidic hot springs; whereas, the archaeal community structure in acidic hot springs was simpler and characterized by Sulfolobales and Thermoplasmata. The phylogenetic analyses showed that Aquificae and Crenarchaeota were predominant in the investigated springs and possessed many phylogenetic lineages that have never been detected in other hot springs in the world. Thus findings from this study significantly improve our understanding of microbial diversity in terrestrial hot springs. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  10. Analysis and exploitation of bacterial population from natural uranium-rich soils: selection of a model specie

    International Nuclear Information System (INIS)

    Mondani, L.

    2010-01-01

    It is well known that soils play a key role in controlling the mobility of toxic metals and this property is greatly influenced by indigenous bacterial communities. This study has been conducted on radioactive and controls soils, collected in natural uraniferous areas (Limousin). A physico-chemical and mineralogical analysis of soils samples was carried out.The structure of bacterial communities was estimated by Denaturing Gradient Gel Electrophoresis (DGGE). The community structure is remarkably more stable in the uranium-rich soils than in the control ones, indicating that uranium exerts a high selection from the soils was constructed and screened for uranium resistance in order to study bacteria-uranium interactions. Scanning electron microscopy revealed that a phylo-genetically diverse set of uranium-resistant species ware able to chelate uranium at the cell surface. (author) [fr

  11. Responses of Ammonia-Oxidising Bacterial Communities to Nitrogen, Lime, and Plant Species in Upland Grassland Soil

    International Nuclear Information System (INIS)

    Rooney, D.C.; Kennedy, N.M.; Clipson, N.J.W.; Rooney, D.C.; Kennedy, N.M.; Gleeson, D.B.

    2010-01-01

    Agricultural improvement of semi natural grasslands has been shown to result in changes to plant and microbial diversity, with consequences for ecosystem functioning. A microcosm approach was used to elucidate the effects of two key components of agricultural improvement (nitrogen addition and liming) on ammonia-oxidising bacterial (AOB) communities in an upland grassland soil. Plant species characteristic of unimproved and improved pastures (A. capillaries and L. perenne) were planted in microcosms, and lime, nitrogen (NH 4 NO 3 ), or lime plus nitrogen added. The AOB community was profiled using terminal restriction fragment length polymorphism (TRFLP) of the amoA gene. AOB community structure was largely altered by NH 4 NO 3 addition, rather than liming, although interactions between nitrogen addition and plant species were also evident. Results indicate that nitrogen addition drives shifts in the structure of key microbial communities in upland grassland soils, and that plant species may play a significant role in determining AOB community structure

  12. An Assessment of Urea-Formaldehyde Fertilizer on the Diversity of Bacterial Communities in Onion and Sugar Beet

    OpenAIRE

    Ikeda, Seishi; Suzuki, Keijiro; Kawahara, Makoto; Noshiro, Masao; Takahashi, Naokazu

    2014-01-01

    The impact of a urea-formaldehyde (UF) fertilizer on bacterial diversity in onion bulbs and main roots of sugar beet were examined using a 16S rRNA gene clone library. The UF fertilizer markedly increased bacterial diversity in both plants. The results of principal coordinates analysis (PCoA) revealed that nearly 30% of the variance observed in bacterial diversity in both the onion and sugar beet was attributed to the fertilization conditions and also that the community structures in both pla...

  13. Analysis of Bacterial Diversity During Acetic Acid Fermentation of Tianjin Duliu Aged Vinegar by 454 Pyrosequencing.

    Science.gov (United States)

    Peng, Qian; Yang, Yanping; Guo, Yanyun; Han, Ye

    2015-08-01

    The vinegar pei harbors complex bacterial communities. Prior studies revealing the bacterial diversity involved were mainly conducted by culture-dependent methods and PCR-DGGE. In this study, 454 pyrosequencing was used to investigate the bacterial communities in vinegar pei during the acetic acid fermentation (AAF) of Tianjin Duliu aged vinegar (TDAV). The results showed that there were 7 phyla and 24 families existing in the vinegar pei, with 2 phyla (Firmicutes, Protebacteria) and 4 families (Lactobacillaceae, Acetobacteracae, Enterobacteriaceae, Chloroplast) predominating. The genus-level identification revealed that 9 genera were the relatively stable, consistent components in different stages of AAF, including the most abundant genus Lactobacillus followed by Acetobacter and Serratia. Additionally, the bacterial community in the early fermentation stage was more complex than those in the later stages, indicating that the accumulation of organic acids provided an appropriate environment to filter unwanted bacteria and to accelerate the growth of required ones. This study provided basic information of bacterial patterns in vinegar pei and relevant changes during AAF of TDAV, and could be used as references in the following study on the implementation of starter culture as well as the improvement of AAF process.

  14. Bacterial diversity in water injection systems of Brazilian offshore oil platforms.

    Science.gov (United States)

    Korenblum, Elisa; Valoni, Erika; Penna, Mônica; Seldin, Lucy

    2010-01-01

    Biogenic souring and microbial-influenced corrosion is a common scenario in water-flooded petroleum reservoirs. Water injection systems are continuously treated to control bacterial contamination, but some bacteria that cause souring and corrosion can persist even after different treatments have been applied. Our aim was to increase our knowledge of the bacterial communities that persist in the water injection systems of three offshore oil platforms in Brazil. To achieve this goal, we used a culture-independent molecular approach (16S ribosomal RNA gene clone libraries) to analyze seawater samples that had been subjected to different treatments. Phylogenetic analyses revealed that the bacterial communities from the different platforms were taxonomically different. A predominance of bacterial clones affiliated with Gammaproteobacteria, mostly belonging to the genus Marinobacter (60.7%), were observed in the platform A samples. Clones from platform B were mainly related to the genera Colwellia (37.9%) and Achromobacter (24.6%), whereas clones obtained from platform C were all related to unclassified bacteria. Canonical correspondence analyses showed that different treatments such as chlorination, deoxygenation, and biocide addition did not significantly influence the bacterial diversity in the platforms studied. Our results demonstrated that the injection water used in secondary oil recovery procedures contained potentially hazardous bacteria, which may ultimately cause souring and corrosion.

  15. Soil-borne bacterial structure and diversity does not reflect community activity in Pampa biome.

    Science.gov (United States)

    Lupatini, Manoeli; Suleiman, Afnan Khalil Ahmad; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Kuramae, Eiko Eurya; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Würdig

    2013-01-01

    The Pampa biome is considered one of the main hotspots of the world's biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.

  16. Rhizosphere bacterial diversity and heavy metal accumulation in Nymphaea pubescens in aid of phytoremediation potential

    Directory of Open Access Journals (Sweden)

    RAISA KABEER

    2014-04-01

    Full Text Available The present work aims to characterize the bacterial diversity of the rhizosphere system of Nymphaea pubescens and the sediment system where it grows naturally. Heavy metal content in the sediment and Nymphea plant from the selected wetland system were also studied. Results of the current study showed that the concentration of copper, zinc and lead in the sediment ranged from 43 to 182 mg/Kg, from 331 to 1382 mg/Kg and from 121 to 1253 mg/Kg, respectively. Cadmium concentration in sediment samples was found to be zero and the order of abundance of heavy metals in the sediment samples was Zn>Pb>Cu>Cd. The abundance patterns of heavy metals in leaf, petiole and root were Cd>Cu>Pb>Zn. Microbial load in rhizosphere of Nymphea pubescens ranged from 93×102 to 69×103 and that of sediment was 62×102 to 125×103. Bacterial load in rhizosphere was higher than that of growing sediment. Four bacterial genera were identified from the rhizosphere of Nymphaea pubescens which include Acinetobacter, Alcaligens, Listeria and Staphylococcus. Acinetobacter, Alcaligens and Listeria are the three bacterial genera isolated from sediment samples. Copper resistance studies of the 14 bacterial isolates from rhizosphere and 7 strains from sediment samples revealed that most of them showed low resistance (<100 μg/ml and very few isolates showed high resistance of 400-500 μg/ml.

  17. Development of a Single Locus Sequence Typing (SLST) Scheme for Typing Bacterial Species Directly from Complex Communities.

    Science.gov (United States)

    Scholz, Christian F P; Jensen, Anders

    2017-01-01

    The protocol describes a computational method to develop a Single Locus Sequence Typing (SLST) scheme for typing bacterial species. The resulting scheme can be used to type bacterial isolates as well as bacterial species directly from complex communities using next-generation sequencing technologies.

  18. Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes

    Science.gov (United States)

    Wemheuer, Franziska; Kaiser, Kristin; Karlovsky, Petr; Daniel, Rolf; Vidal, Stefan; Wemheuer, Bernd

    2017-01-01

    Endophytic bacteria are critical for plant growth and health. However, compositional and functional responses of bacterial endophyte communities towards agricultural practices are still poorly understood. Hence, we analyzed the influence of fertilizer application and mowing frequency on bacterial endophytes in three agriculturally important grass species. For this purpose, we examined bacterial endophytic communities in aerial plant parts of Dactylis glomerata L., Festuca rubra L., and Lolium perenne L. by pyrotag sequencing of bacterial 16S rRNA genes over two consecutive years. Although management regimes influenced endophyte communities, observed responses were grass species-specific. This might be attributed to several bacteria specifically associated with a single grass species. We further predicted functional profiles from obtained 16S rRNA data. These profiles revealed that predicted abundances of genes involved in plant growth promotion or nitrogen metabolism differed between grass species and between management regimes. Moreover, structural and functional community patterns showed no correlation to each other indicating that plant species-specific selection of endophytes is driven by functional rather than phylogenetic traits. The unique combination of 16S rRNA data and functional profiles provided a holistic picture of compositional and functional responses of bacterial endophytes in agricultural relevant grass species towards management practices.

  19. National survey of molecular bacterial diversity of New Zealand groundwater: relationships between biodiversity, groundwater chemistry and aquifer characteristics.

    Science.gov (United States)

    Sirisena, Kosala A; Daughney, Christopher J; Moreau-Fournier, Magali; Ryan, Ken G; Chambers, Geoffrey K

    2013-12-01

    Groundwater is a vital component of rural and urban water supplies in New Zealand. Although extensive monitoring of chemical and physical properties is conducted due to the high demand for this valuable resource, current information on its bacterial content is limited. However, bacteria provide an immense contribution to drive the biogeochemical processes in the groundwater ecosystem as in any other ecosystem. Therefore, a proper understanding of bacterial diversity is crucial to assess the effectiveness of groundwater management policies. In this study, we investigated the bacterial community structure in NZ groundwater at a national scale using the terminal restriction fragment length polymorphism (T-RFLP) molecular profiling tool and determined the relationships between bacterial diversity and groundwater chemistry, geological parameters and human impact. Considerable bacterial diversity was present and the community structures were strongly related to groundwater chemistry, and in particular to redox potential and human impact, reflecting their potential influence on determination of bacterial diversity. Further, the mean residence time of groundwater also showed relationships with bacterial community structure. These novel findings pertaining to community composition and its relationships with environmental parameters will provide a strong foundation for qualitative exploration of the bacterial diversity in NZ groundwater in relation to sustainable management of this valuable resource. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  20. Prospects of molecular markers in Fusarium species diversity

    DEFF Research Database (Denmark)

    Nayaka, S. Chandra; Wulff, Ednar Gadelha; Udayashankar, A.C.

    2011-01-01

    focuses of various molecular-based techniques employed to study the diversity of Fusarium species causing diseases in major food crops. An introduction of fusarial diseases and their mycotoxins and molecular-marker-based methods for detection introduce the concept of marker application. Various well...... for generation of probes and their use in phylogeny of Fusarium spp. are also presented. The concluding part emphasizes the value of molecular markers for assessing genetic variability and reveals that molecular tools are indispensable for providing information not only of one Fusarium species but on whole......-known molecular techniques such as random amplified polymorphic DNA, amplification fragment length polymorphism, etc. to more modern ones such as DNA microarrays, DNA barcoding, and pyrosequencing and their application form the core of the review. Target regions in the genome which can be potential candidates...

  1. Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes

    Directory of Open Access Journals (Sweden)

    Ditte V. Vestergaard

    2018-05-01

    Full Text Available Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building’s occupants. A major example is the decreased diversity and altered composition of indoor airborne microbial communities as a proposed explanation for the increasing prevalence of asthma and allergies worldwide. Previous research has shown that living on a farm confers protection against development of asthma and allergies, with airborne bacteria suggested as playing a role in this protective effect. However, the composition of this beneficial microbial community has still not been identified. We sampled settled airborne dust using a passive dust sampler from Danish pig stables, associated farmers’ homes, and from suburban homes (267 samples in total and carried out quantitative PCR measurements of bacterial abundance and MiSeq sequencing of the V3–V4 region of bacterial 16S rRNA genes found in these samples. Airborne bacteria had a greater diversity and were significantly more abundant in pig stables and farmers’ homes than suburban homes (Wilcoxon rank sum test P < 0.05. Moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers’ homes than in suburban homes (ALDEx2 with P < 0.05, including Firmicutes, Peptostreptococcaceae, Prevotellaceae, Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, and Lactobacillus. Pig stables had significantly lower airborne bacterial diversity than farmers’ homes, and there was no discernable direct transfer of airborne bacteria from stable to home. This study identifies differences in indoor airborne bacterial communities that may be an important component of this putative protective effect, while showing that pig stables

  2. Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes

    Science.gov (United States)

    Vestergaard, Ditte V.; Holst, Gitte J.; Basinas, Ioannis; Elholm, Grethe; Schlünssen, Vivi; Linneberg, Allan; Šantl-Temkiv, Tina; Finster, Kai; Sigsgaard, Torben; Marshall, Ian P. G.

    2018-01-01

    Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building’s occupants. A major example is the decreased diversity and altered composition of indoor airborne microbial communities as a proposed explanation for the increasing prevalence of asthma and allergies worldwide. Previous research has shown that living on a farm confers protection against development of asthma and allergies, with airborne bacteria suggested as playing a role in this protective effect. However, the composition of this beneficial microbial community has still not been identified. We sampled settled airborne dust using a passive dust sampler from Danish pig stables, associated farmers’ homes, and from suburban homes (267 samples in total) and carried out quantitative PCR measurements of bacterial abundance and MiSeq sequencing of the V3–V4 region of bacterial 16S rRNA genes found in these samples. Airborne bacteria had a greater diversity and were significantly more abundant in pig stables and farmers’ homes than suburban homes (Wilcoxon rank sum test P < 0.05). Moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers’ homes than in suburban homes (ALDEx2 with P < 0.05), including Firmicutes, Peptostreptococcaceae, Prevotellaceae, Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, and Lactobacillus. Pig stables had significantly lower airborne bacterial diversity than farmers’ homes, and there was no discernable direct transfer of airborne bacteria from stable to home. This study identifies differences in indoor airborne bacterial communities that may be an important component of this putative protective effect, while showing that pig stables themselves do not appear

  3. Approach to determine the diversity of Legionella species by nested PCR-DGGE in aquatic environments

    Science.gov (United States)

    Huang, Wen-Chien; Tsai, Hsin-Chi; Tao, Chi-Wei; Chen, Jung-Sheng; Shih, Yi-Jia; Kao, Po-Min; Huang, Tung-Yi; Hsu, Bing-Mu

    2017-01-01

    In this study, we describe a nested PCR-DGGE strategy to detect Legionella communities from river water samples. The nearly full-length 16S rRNA gene was amplified using bacterial primer in the first step. After, the amplicons were employed as DNA templates in the second PCR using Legionella specific primer. The third round of gene amplification was conducted to gain PCR fragments apposite for DGGE analysis. Then the total numbers of amplified genes were observed in DGGE bands of products gained with primers specific for the diversity of Legionella species. The DGGE patterns are thus potential for a high-throughput preliminary determination of aquatic environmental Legionella species before sequencing. Comparative DNA sequence analysis of excised DGGE unique band patterns showed the identity of the Legionella community members, including a reference profile with two pathogenic species of Legionella strains. In addition, only members of Legionella pneumophila and uncultured Legionella sp. were detected. Development of three step nested PCR-DGGE tactic is seen as a useful method for studying the diversity of Legionella community. The method is rapid and provided sequence information for phylogenetic analysis. PMID:28166249

  4. Genetic Diversity of Some Capparis L. Species Growing in Syria

    Directory of Open Access Journals (Sweden)

    Bassam Al- Safadi

    2014-12-01

    Full Text Available This work investigated the genetic diversity and relationships among Capparis species growing in Syria using IRAP and ISSR techniques. Forty-seven samples of three Capparis species genotypes were collected from 21 different locations in Syria. The genotypes were morphologically identified based on the descriptions available in the literature. When IRAP technique was used, an average of 71.5% of the amplified fragments were polymorphic compared to 82.04% in ISSR. Morphological characterization along with the cluster and PCoA analyses of the data divided the studied genotypes into three groups. The groups included genotypes identified as Capparis spinosa L, C. sicula Duh., and C. aegyptia Lam. Based on the morphological description, molecular studies and statistical analyses of this study, C. aegyptia could be suggested as a separate species and not a varietal rank of C. spinosa(C. spinosa var. aegyptia (Lam.. Two samples (Alep1 and Idl were not placed in any of the three distinctive groups, despite their closeness morphologically to C. spinosa. In PCoA analysis, sample Alep1 came between C. sicula and C. spinosa and Idl was placed between C. sicula and C. aegyptia. Although hybridization between Capparis species could occur, it was not clear from the present study if these two genotypes were hybrids.

  5. Bacterial diversity and community structure of supragingival plaques in adults with dental health or caries revealed by 16S pyrosequencing

    Directory of Open Access Journals (Sweden)

    Cuicui Xiao

    2016-07-01

    Full Text Available Dental caries has a polymicrobial etiology within the complex oral microbial ecosystem. However, the overall diversity and structure of supragingival plaque microbiota in adult dental health and caries are not well understood. Here, 160 supragingival plaque samples from patients with dental health and different severities of dental caries were collected for bacterial genomic DNA extraction, pyrosequencing by amplification of the 16S rDNA V1–V3 hypervariable regions, and bioinformatic analysis. High-quality sequences (2,261,700 clustered into 10,365 operational taxonomic units (OTUs; 97% identity, representing 453 independent species belonging to 122 genera, 66 families, 34 orders, 21 classes, and 12 phyla. All groups shared 7522 OTUs, indicating the presence of a core plaque microbiome. Smooth rarefaction curves were suggestive of plaque microbial diversity. α diversity analysis showed that healthy plaque microbial diversity exceeded that of dental caries, with the diversity decreasing gradually with the severity of caries. The dominant phyla of plaque microbiota included Bacteroidetes, Actinobacteria, Proteobacteria, Firmicutes, Fusobacteria, and TM7. The dominant genera included Capnocytophaga, Prevotella, Actinomyces, Corynebacterium, Neisseria, Streptococcus, Rothia, and Leptotrichia. β diversity analysis showed that the plaque microbial community structure was similar in all groups and that group members were relatively constant, only showing differences in abundance. Analysis of composition differences identified 10 health-related and 21 caries-related genera. Key genera (27 that potentially contributed to plaque microbiota distributions between groups were identified. Finally, co-occurrence network analysis and function prediction were performed. Treatment strategies directed toward modulating microbial interactions and their functional output should be further developed.

  6. Genetic diversity of citrus bacterial canker pathogens preserved in herbarium specimens.

    Science.gov (United States)

    Li, Wenbin; Song, Qijian; Brlansky, Ronald H; Hartung, John S

    2007-11-20

    Citrus bacterial canker (CBC) caused by Xanthomonas axonopodis pv. citri (Xac) was first documented in India and Java in the mid 19th century. Since that time, the known distribution of the disease has steadily increased. Concurrent with the dispersion of the pathogen, the diversity of described strains continues to increase, with novel strains appearing in Saudi Arabia, Iran, and Florida in the last decade. Herbarium specimens of infected plants provide an historical record documenting both the geographic distribution and genetic diversity of the pathogen in the past. However, no method was available to assess the genetic diversity within these herbarium samples. We have developed a method, insertion event scanning (IES), and applied the method to characterize the diversity present within CBC populations documented as herbarium specimens over the past century. IES is based on the specific amplification of junction fragments that define insertion events. The potential for IES in current forensic applications is demonstrated by finding an exact match of pathogen genotypes preserved in herbarium specimens from Japan and Florida, demonstrating the source of the original outbreak of citrus canker in Florida in 1911. IES is a very sensitive technique for differentiating bacterial strains and can be applied to any of the several hundred bacteria for which full genomic sequence data are available.

  7. Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

    Directory of Open Access Journals (Sweden)

    Mariana Gomes Germano

    2012-05-01

    Full Text Available The objective of this work was to evaluate the catabolic gene diversity for the bacterial degradation of aromatic hydrocarbons in anthropogenic dark earth of Amazonia (ADE and their biochar (BC. Functional diversity analyses in ADE soils can provide information on how adaptive microorganisms may influence the fertility of soils and what is their involvement in biogeochemical cycles. For this, clone libraries containing the gene encoding for the alpha subunit of aromatic ring-hydroxylating dioxygenases (α-ARHD bacterial gene were constructed, totaling 800 clones. These libraries were prepared from samples of an ADE soil under two different land uses, located at the Caldeirão Experimental Station - secondary forest (SF and agriculture (AG -, and the biochar (SF_BC and AG_BC, respectively. Heterogeneity estimates indicated greater diversity in BC libraries; and Venn diagrams showed more unique operational protein clusters (OPC in the SF_BC library than the ADE soil, which indicates that specific metabolic processes may occur in biochar. Phylogenetic analysis showed unidentified dioxygenases in ADE soils. Libraries containing functional gene encoding for the alpha subunit of the aromatic ring-hydroxylating dioxygenases (ARHD gene from biochar show higher diversity indices than those of ADE under secondary forest and agriculture.

  8. Towards large-scale FAME-based bacterial species identification using machine learning techniques.

    Science.gov (United States)

    Slabbinck, Bram; De Baets, Bernard; Dawyndt, Peter; De Vos, Paul

    2009-05-01

    In the last decade, bacterial taxonomy witnessed a huge expansion. The swift pace of bacterial species (re-)definitions has a serious impact on the accuracy and completeness of first-line identification methods. Consequently, back-end identification libraries need to be synchronized with the List of Prokaryotic names with Standing in Nomenclature. In this study, we focus on bacterial fatty acid methyl ester (FAME) profiling as a broadly used first-line identification method. From the BAME@LMG database, we have selected FAME profiles of individual strains belonging to the genera Bacillus, Paenibacillus and Pseudomonas. Only those profiles resulting from standard growth conditions have been retained. The corresponding data set covers 74, 44 and 95 validly published bacterial species, respectively, represented by 961, 378 and 1673 standard FAME profiles. Through the application of machine learning techniques in a supervised strategy, different computational models have been built for genus and species identification. Three techniques have been considered: artificial neural networks, random forests and support vector machines. Nearly perfect identification has been achieved at genus level. Notwithstanding the known limited discriminative power of FAME analysis for species identification, the computational models have resulted in good species identification results for the three genera. For Bacillus, Paenibacillus and Pseudomonas, random forests have resulted in sensitivity values, respectively, 0.847, 0.901 and 0.708. The random forests models outperform those of the other machine learning techniques. Moreover, our machine learning approach also outperformed the Sherlock MIS (MIDI Inc., Newark, DE, USA). These results show that machine learning proves very useful for FAME-based bacterial species identification. Besides good bacterial identification at species level, speed and ease of taxonomic synchronization are major advantages of this computational species

  9. Distribution, diversity and abundance of bacterial laccase-like genes in different particle size fractions of sediments in a subtropical mangrove ecosystem.

    Science.gov (United States)

    Luo, Ling; Zhou, Zhi-Chao; Gu, Ji-Dong

    2015-10-01

    This study investigated the diversity and abundance of bacterial lacasse-like genes in different particle size fractions, namely sand, silt, and clay of sediments in a subtropical mangrove ecosystem. Moreover, the effects of nutrient conditions on bacterial laccase-like communities as well as the correlation between nutrients and, both the abundance and diversity indices of laccase-like bacteria in particle size fractions were also studied. Compared to bulk sediments, Bacteroidetes, Caldithrix, Cyanobacteria and Chloroflexi were dominated in all 3 particle-size fractions of intertidal sediment (IZ), but Actinobacteria and Firmicutes were lost after the fractionation procedures used. The diversity index of IZ fractions decreased in the order of bulk > clay > silt > sand. In fractions of mangrove forest sediment (MG), Verrucomicrobia was found in silt, and both Actinobacteria and Bacteroidetes appeared in clay, but no new species were found in sand. The declining order of diversity index in MG fractions was clay > silt > sand > bulk. Furthermore, the abundance of lacasse-like bacteria varied with different particle-size fractions significantly (p clay > silt in both IZ and MG fractions. Additionally, nutrient availability was found to significantly affect the diversity and community structure of laccase-like bacteria (p fractions (p < 0.05). Therefore, this study further provides evidence that bacterial laccase plays a vital role in turnover of sediment organic matter and cycling of nutrients.

  10. Differences in Bacterial Diversity and Communities Between Glacial Snow and Glacial Soil on the Chongce Ice Cap, West Kunlun Mountains.

    Science.gov (United States)

    Yang, Guang Li; Hou, Shu Gui; Le Baoge, Ri; Li, Zhi Guo; Xu, Hao; Liu, Ya Ping; Du, Wen Tao; Liu, Yong Qin

    2016-11-04

    A detailed understanding of microbial ecology in different supraglacial habitats is important due to the unprecedented speed of glacier retreat. Differences in bacterial diversity and community structure between glacial snow and glacial soil on the Chongce Ice Cap were assessed using 454 pyrosequencing. Based on rarefaction curves, Chao1, ACE, and Shannon indices, we found that bacterial diversity in glacial snow was lower than that in glacial soil. Principal coordinate analysis (PCoA) and heatmap analysis indicated that there were major differences in bacterial communities between glacial snow and glacial soil. Most bacteria were different between the two habitats; however, there were some common bacteria shared between glacial snow and glacial soil. Some rare or functional bacterial resources were also present in the Chongce Ice Cap. These findings provide a preliminary understanding of the shifts in bacterial diversity and communities from glacial snow to glacial soil after the melting and inflow of glacial snow into glacial soil.

  11. Longitudinal shifts in bacterial diversity and fermentation pattern in the rumen of steers grazing wheat pasture.

    Science.gov (United States)

    Pitta, D W; Pinchak, W E; Dowd, S; Dorton, K; Yoon, I; Min, B R; Fulford, J D; Wickersham, T A; Malinowski, D P

    2014-12-01

    Grazing steers on winter wheat forage is routinely practiced in the Southern Great Plains of the US. Here, we investigated the dynamics in bacterial populations of both solid and liquid ruminal fractions of steers grazing on maturing wheat forage of changing nutritive quality. The relationship between bacterial diversity and fermentation parameters in the liquid fraction was also investigated. During the first 28 days, the wheat was in a vegetative phase with a relatively high crude protein content (CP; 21%), which led to the incidence of mild cases of frothy bloat among steers. Rumen samples were collected on days 14, 28, 56 and 76, separated into solid and liquid fractions and analyzed for bacterial diversity using 16S pyrotag technology. The predominant phyla identified were Bacteroidetes (59-77%) and Firmicutes (20-33%) across both ruminal fractions. Very few differences were observed in the rumen bacterial communities within solid and liquid fractions on day 14. However, by day 28, the relatively high CP content complemented a distinct bacterial and chemical composition of the rumen fluid that was characterized by a higher ratio (4:1) of Bacteroidetes:Firmicutes and a corresponding lower acetate:propionate (3:1) ratio. Further, a greater accumulation of biofilm (mucopolysaccharide complex) on day 28 was strongly associated with the abundance of Firmicutes lineages such as Clostridium, Ruminococcus, Oscillospira and Moryella (Prumen microbiome and their association with fermentation activity in the rumen of steers during the vegetative (bloat-prone) and reproductive stages of wheat forage. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Smokeless tobacco products harbor diverse bacterial microbiota that differ across products and brands.

    Science.gov (United States)

    Smyth, Eoghan M; Kulkarni, Prachi; Claye, Emma; Stanfill, Stephen; Tyx, Robert; Maddox, Cynthia; Mongodin, Emmanuel F; Sapkota, Amy R

    2017-07-01

    Smokeless tobacco products contain numerous chemical compounds, including known human carcinogens. Other smokeless tobacco constituents, including bacteria, may also contribute to adverse health effects among smokeless tobacco users. However, there is a lack of data regarding the microbial constituents of smokeless tobacco. Our goal was to characterize the bacterial microbiota of different smokeless tobacco products and evaluate differences across product types and brands. DNA was extracted from 15 brands of smokeless tobacco products (including dry snuff, moist snuff, snus, and Swedish snus) and 6 handmade products (e.g., toombak) using an enzymatic and mechanical lysis approach. Bacterial community profiling was performed using PCR amplification of the V1-V2 hypervariable region of the 16S rRNA gene, followed by 454 pyrosequencing of the resulting amplicons and sequence analysis using the QIIME package. Total viable counts were also determined to estimate the number of viable bacteria present in each product. Average total viable counts ranged from 0 to 9.35 × 10 7  CFU g -1 . Analysis of the 16S rRNA gene sequences revealed high bacterial diversity across the majority of products tested: dry snuff products where characterized by the highest diversity indices compared to other products. The most dominant bacterial phyla across all products were Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Significant differences in both bacterial community composition and in silico predicted gene content were observed between smokeless tobacco product types and between brands of specific smokeless tobacco products. These data are useful in order to comprehensively address potential health risks associated with the use of smokeless tobacco products.

  13. Transcriptional responses of Treponema denticola to other oral bacterial species.

    Directory of Open Access Journals (Sweden)

    Juni Sarkar

    Full Text Available The classic organization by Socransky and coworkers categorized the oral bacteria of the subgingival plaque into different complexes. Treponema denticola, Porphyromonas gingivalis and Tannerella forsythia are grouped into the red complex that is highly correlated with periodontal disease. Socransky's work closely associates red with orange complex species such as Fusobacterium nucleatum and Prevotella intermedia but not with members of the other complexes. While the relationship between species contained by these complexes is in part supported by their ability to physically attach to each other, the physiological consequences of these interactions and associations are less clear. In this study, we employed T. denticola as a model organism to analyze contact-dependent responses to interactions with species belonging to the same complex (P. gingivalis and T. forsythia, the closely associated orange complex (using F. nucleatum and P. intermedia as representatives and the unconnected yellow complex (using Streptococcus sanguinis and S. gordonii as representatives. RNA was extracted from T. denticola alone as well as after pairwise co-incubation for 5 hrs with representatives of the different complexes, and the respective gene expression profiles were determined using microarrays. Numerous genes related to motility, metabolism, transport, outer membrane and hypothetical proteins were differentially regulated in T. denticola in the presence of the tested partner species. Further analysis revealed a significant overlap in the affected genes and we identified a general response to the presence of other species, those specific to two of the three complexes as well as individual complexes. Most interestingly, many predicted major antigens (e.g. flagella, Msp, CTLP were suppressed in responses that included red complex species indicating that the presence of the most closely associated species induces immune-evasive strategies. In summary, the data

  14. Changes in bacterial diversity associated with bioremediation of used lubricating oil in tropical soils.

    Science.gov (United States)

    Meeboon, Naruemon; Leewis, Mary-Cathrine; Kaewsuwan, Sireewan; Maneerat, Suppasil; Leigh, Mary Beth

    2017-08-01

    Used lubricating oil (ULO) is a widespread contaminant, particularly throughout tropical regions, and may be a candidate for bioremediation. However, little is known about the biodegradation potential or basic microbial ecology of ULO-contaminated soils. This study aims to determine the effects of used ULO on bacterial community structure and diversity. Using a combination of culture-based (agar plate counts) and molecular techniques (16S rRNA gene sequencing and DGGE), we investigated changes in soil bacterial communities from three different ULO-contaminated soils collected from motorcycle mechanical workshops (soil A, B, and C). We further explored the relationship between bacterial community structure, physiochemical soil parameters, and ULO composition in three ULO-contaminated soils. Results indicated that the three investigated soils had different community structures, which may be a result of the different ULO characteristics and physiochemical soil parameters of each site. Soil C had the highest ULO concentration and also the greatest diversity and richness of bacteria, which may be a result of higher nutrient retention, organic matter and cation exchange capacity, as well as freshness of oil compared to the other soils. In soils A and B, Proteobacteria (esp. Gammaproteobacteria) dominated the bacterial community, and in soil C, Actinobacteria and Firmicutes dominated. The genus Enterobacter, a member of the class Gammaproteobacteria, is known to include ULO-degraders, and this genus was the only one found in all three soils, suggesting that it could play a key role in the in situ degradation of ULO-contaminated tropical Thai soils. This study provides insights into our understanding of soil microbial richness, diversity, composition, and structure in tropical ULO-contaminated soils, and may be useful for the development of strategies to improve bioremediation.

  15. Long-term nickel exposure altered the bacterial community composition but not diversity in two contrasting agricultural soils.

    Science.gov (United States)

    Li, Jing; Hu, Hang-Wei; Ma, Yi-Bing; Wang, Jun-Tao; Liu, Yu-Rong; He, Ji-Zheng

    2015-07-01

    Nickel pollution imposes deleterious effects on soil ecosystem. The responses of soil microorganisms to long-term nickel pollution under field conditions remain largely unknown. Here, we used high-throughput sequencing to elucidate the impacts of long-term nickel pollution on soil bacterial communities in two contrasting agricultural soils. Our results found that the soil microbial biomass carbon consistently decreased along the nickel gradients in both soils. Nickel pollution selectively favored or impeded the prevalence of several dominant bacterial guilds, in particular, Actinobacteria showed tolerance, while Acidobacteria and Planctomycetes displayed sensitivity. Despite the apparent shifts in the bacterial community composition, no clear tendency in the bacterial diversity and abundance was identified along the nickel gradients in either soil. Collectively, we provide evidence that long-term nickel pollution shifted the soil bacterial communities, resulting in the decrease of microbial biomass although the bacterial diversity was not significantly changed.

  16. Bacterial diversity and their adaptations in the shallow water hydrothermal vent at D. Joao de Castro Seamount (DJCS), Azores, Portugal

    Digital Repository Service at National Institute of Oceanography (India)

    Mohandass, C.; Rajasabapathy, R.; Ravindran, C.; Colaco, A.; Santos, R.S.; Meena, R.M.

    Bacterial diversity investigations were made from the shallow vent of D joao de castro, Azores, Portugal and their adaptations to a nutrient rich environment was investigated from 2004 and 2005 cruise samples. Assesment of the qualitative...

  17. Genetic diversity among and within cultured cyanobionts of diverse species of Azolla.

    Science.gov (United States)

    Sood, A; Prasanna, R; Prasanna, B M; Singh, P K

    2008-01-01

    The cyanobionts isolated from 10 Azolla accessions belonging to 6 species (Azolla mexicana, A. microphylla, A. rubra, A. caroliniana, A. filiculoides, A. pinnata) were cultured under laboratory conditions and analyzed on the basis of whole cell protein profiles and molecular marker dataset generated using repeat sequence primers (STRR(mod) and HipTG). The biochemical and molecular marker profiles of the cyanobionts were compared with those of the free-living cyanobacteria and symbiotic Nostoc strains from Anthoceros sp., Cycas sp. and Gunnera monoika. Cluster analysis revealed the genetic diversity among the selected strains, and identified 3 distinct clusters. Group 1 included cyanobionts from all the 10 accessions of Azolla, group 2 comprised all the symbiotic Nostoc strains, while group 3 included the free-living cyanobacteria belonging to the genera Nostoc and Anabaena. The interrelationships among the Azolla cyanobionts were further revealed by principal component analysis. Cyanobionts from A. caroliniana-A. microphylla grouped together while cyanobionts associated with A. mexicana-A. filiculoides along with A. pinnata formed another group. A. rubra cyanobionts had intermediate relationship with both the subgroups. This is the first study analyzing the diversity existing among the cultured cyanobionts of diverse Azolla species through the use of biochemical and molecular profiles and also the genetic distinctness of these free-living cyanobionts as compared to cyanobacterial strains of the genera Anabaena and Nostoc.

  18. Diversity of Dominant Bacterial Taxa in Activated Sludge Promotes Functional Resistance following Toxic Shock Loading

    KAUST Repository

    Saikaly, Pascal

    2010-12-14

    Examining the relationship between biodiversity and functional stability (resistance and resilience) of activated sludge bacterial communities following disturbance is an important first step towards developing strategies for the design of robust biological wastewater treatment systems. This study investigates the relationship between functional resistance and biodiversity of dominant bacterial taxa by subjecting activated sludge samples, with different levels of biodiversity, to toxic shock loading with cupric sulfate (Cu[II]), 3,5-dichlorophenol (3,5-DCP), or 4-nitrophenol (4-NP). Respirometric batch experiments were performed to determine the functional resistance of activated sludge bacterial community to the three toxicants. Functional resistance was estimated as the 30 min IC50 or the concentration of toxicant that results in a 50% reduction in oxygen utilization rate compared to a referential state represented by a control receiving no toxicant. Biodiversity of dominant bacterial taxa was assessed using polymerase chain reaction-terminal restriction fragment length polymorphism (PCR-T-RFLP) targeting the 16S ribosomal RNA (16S rRNA) gene. Statistical analysis of 30 min IC50 values and PCR-T-RFLP data showed a significant positive correlation (P<0.05) between functional resistance and microbial diversity for each of the three toxicants tested. To our knowledge, this is the first study showing a positive correlation between biodiversity of dominant bacterial taxa in activated sludge and functional resistance. In this system, activated sludge bacterial communities with higher biodiversity are functionally more resistant to disturbance caused by toxic shock loading. © 2010 Springer Science+Business Media, LLC.

  19. Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean.

    Science.gov (United States)

    Li, Yuan-Yuan; Chen, Xiao-Huang; Xie, Zhang-Xian; Li, Dong-Xu; Wu, Peng-Fei; Kong, Ling-Fen; Lin, Lin; Kao, Shuh-Ji; Wang, Da-Zhi

    2018-01-01

    Nitrogen (N) is a primary limiting nutrient for bacterial growth and productivity in the ocean. To better understand bacterial community and their N utilization strategy in different N regimes of the ocean, we examined bacterial diversity, diazotrophic diversity, and N utilization gene expressions in the northwestern Pacific Ocean (NWPO) using a combination of high-throughput sequencing and real-time qPCR methods. 521 and 204 different operational taxonomic units (OTUs) were identified in the 16s rRNA and nifH libraries from nine surface samples. Of the 16s rRNA gene OTUs, 11.9% were observed in all samples while 3.5 and 15.9% were detected only in N-sufficient and N-deficient samples. Proteobacteria, Cyanobacteria and Bacteroidetes dominated the bacterial community. Prochlorococcus and Pseudoalteromonas were the most abundant at the genus level in N-deficient regimes, while SAR86, Synechococcus and SAR92 were predominant in the Kuroshio-Oyashio confluence region. The distribution of the nifH gene presented great divergence among sampling stations: Cyanobacterium_UCYN-A dominated the N-deficient stations, while clusters related to the Alpha-, Beta- , and Gamma-Proteobacteria were abundant in other stations. Temperature was the main factor that determined bacterial community structure and diversity while concentration of NO X -N was significantly correlated with structure and distribution of N 2 -fixing microorganisms. Expression of the ammonium transporter was much higher than that of urea transporter subunit A ( urtA ) and ferredoxin-nitrate reductase , while urtA had an increased expression in N-deficient surface water. The predicted ammonium transporter and ammonium assimilation enzymes were most abundant in surface samples while urease and nitrogenase were more abundant in the N-deficient regions. These findings underscore the fact that marine bacteria have evolved diverse N utilization strategies to adapt to different N habitats, and that urea metabolism is of

  20. Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean

    Directory of Open Access Journals (Sweden)

    Yuan-Yuan Li

    2018-04-01

    Full Text Available Nitrogen (N is a primary limiting nutrient for bacterial growth and productivity in the ocean. To better understand bacterial community and their N utilization strategy in different N regimes of the ocean, we examined bacterial diversity, diazotrophic diversity, and N utilization gene expressions in the northwestern Pacific Ocean (NWPO using a combination of high-throughput sequencing and real-time qPCR methods. 521 and 204 different operational taxonomic units (OTUs were identified in the 16s rRNA and nifH libraries from nine surface samples. Of the 16s rRNA gene OTUs, 11.9% were observed in all samples while 3.5 and 15.9% were detected only in N-sufficient and N-deficient samples. Proteobacteria, Cyanobacteria and Bacteroidetes dominated the bacterial community. Prochlorococcus and Pseudoalteromonas were the most abundant at the genus level in N-deficient regimes, while SAR86, Synechococcus and SAR92 were predominant in the Kuroshio-Oyashio confluence region. The distribution of the nifH gene presented great divergence among sampling stations: Cyanobacterium_UCYN-A dominated the N-deficient stations, while clusters related to the Alpha-, Beta-, and Gamma-Proteobacteria were abundant in other stations. Temperature was the main factor that determined bacterial community structure and diversity while concentration of NOX-N was significantly correlated with structure and distribution of N2-fixing microorganisms. Expression of the ammonium transporter was much higher than that of urea transporter subunit A (urtA and ferredoxin-nitrate reductase, while urtA had an increased expression in N-deficient surface water. The predicted ammonium transporter and ammonium assimilation enzymes were most abundant in surface samples while urease and nitrogenase were more abundant in the N-deficient regions. These findings underscore the fact that marine bacteria have evolved diverse N utilization strategies to adapt to different N habitats, and that urea

  1. [Bacterial diversity in sequencing batch biofilm reactor (SBBR) for landfill leachate treatment using PCR-DGGE].

    Science.gov (United States)

    Xiao, Yong; Yang, Zhao-hui; Zeng, Guang-ming; Ma, Yan-he; Liu, You-sheng; Wang, Rong-juan; Xu, Zheng-yong

    2007-05-01

    For studying the bacterial diversity and the mechanism of denitrification in sequencing bath biofilm reactor (SBBR) treating landfill leachate to provide microbial evidence for technique improvements, total microbial DNA was extracted from samples which were collected from natural landfill leachate and biofilm of a SBBR that could efficiently remove NH4+ -N and COD of high concentration. 16S rDNA fragments were amplified from the total DNA successfully using a pair of universal bacterial 16S rDNA primer, GC341F and 907R, and then were used for denaturing gradient gel electrophoresis (DGGE) analysis. The bands in the gel were analyzed by statistical methods and excided from the gel for sequencing, and the sequences were used for homology analysis and then two phylogenetic trees were constructed using DNAStar software. Results indicated that the bacterial diversity of the biofilm in SBBR and the landfill leachate was abundant, and no obvious change of community structure happened during running in the biofilm, in which most bacteria came from the landfill leachate. There may be three different modes of denitrification in the reactor because several different nitrifying bacteria, denitrifying bacteria and anaerobic ammonia oxidation bacteria coexisted in it. The results provided some valuable references for studying microbiological mechanism of denitrification in SBBR.

  2. Bacterial diversity of Taxus rhizosphere: culture-independent and culture-dependent approaches.

    Science.gov (United States)

    Hao, Da Cheng; Ge, Guang Bo; Yang, Ling

    2008-07-01

    The regional variability of Taxus rhizosphere bacterial community composition and diversity was studied by comparative analysis of three large 16S rRNA gene clone libraries from the Taxus rhizosphere in different regions of China (subtropical and temperate regions). One hundred and forty-six clones were screened for three libraries. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the abundance of sequences affiliated with Gammaproteobacteria, Betaproteobacteria, and Actinobacteria was higher in the library from the T. xmedia rhizosphere of the temperate region compared with the subtropical Taxus mairei rhizosphere. On the other hand, Acidobacteria was more abundant in libraries from the subtropical Taxus mairei rhizosphere. Richness estimates and diversity indices of three libraries revealed major differences, indicating a higher richness in the Taxus rhizosphere bacterial communities of the subtropical region and considerable variability in the bacterial community composition within this region. By enrichment culture, a novel Actinobacteria strain DICP16 was isolated from the T. xmedia rhizosphere of the temperate region and was identified as Leifsonia shinshuensis sp. via 16S rRNA gene and gyrase B sequence analyses. DICP16 was able to remove the xylosyl group from 7-xylosyl-10-deacetylbaccatin III and 7-xylosyl-10-deacetylpaclitaxel, thereby making the xylosyltaxanes available as sources of 10-deacetylbaccatin III and the anticancer drug paclitaxel. Taken together, the present studies provide, for the first time, the knowledge of the biodiversity of microorganisms populating Taxus rhizospheres.

  3. Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

    Directory of Open Access Journals (Sweden)

    Gendrault-Jacquemard A

    2005-07-01

    Full Text Available Abstract Background Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. Results Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. Conclusion The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.

  4. Evidence of diversity and recombination in Arsenophonus symbionts of the Bemisia tabaci species complex

    Directory of Open Access Journals (Sweden)

    Mouton Laurence

    2012-01-01

    Full Text Available Abstract Background Maternally inherited bacterial symbionts infecting arthropods have major implications on host ecology and evolution. Among them, the genus Arsenophonus is particularly characterized by a large host spectrum and a wide range of symbiotic relationships (from mutualism to parasitism, making it a good model to study the evolution of host-symbiont associations. However, few data are available on the diversity and distribution of Arsenophonus within host lineages. Here, we propose a survey on Arsenophonus diversity in whitefly species (Hemiptera, in particular the Bemisia tabaci species complex. This polyphagous insect pest is composed of genetic groups that differ in many ecological aspects. They harbor specific bacterial communities, among them several lineages of Arsenophonus, enabling a study of the evolutionary history of these bacteria at a fine host taxonomic level, in association to host geographical range and ecology. Results Among 152 individuals, our analysis identified 19 allelic profiles and 6 phylogenetic groups, demonstrating this bacterium's high diversity. These groups, based on Arsenophonus phylogeny, correlated with B. tabaci genetic groups with two exceptions reflecting horizontal transfers. None of three genes analyzed provided evidence of intragenic recombination, but intergenic recombination events were detected. A mutation inducing a STOP codon on one gene in a strain infecting one B. tabaci genetic group was also found. Phylogenetic analyses of the three concatenated loci revealed the existence of two clades of Arsenophonus. One, composed of strains found in other Hemiptera, could be the ancestral clade in whiteflies. The other, which regroups strains found in Hymenoptera and Diptera, may have been acquired more recently by whiteflies through lateral transfers. Conclusions This analysis of the genus Arsenophonus revealed a diversity within the B. tabaci species complex which resembles that reported on the

  5. Cholesterol gallstones and bile host diverse bacterial communities with potential to promote the formation of gallstones.

    Science.gov (United States)

    Peng, Yuhong; Yang, Yang; Liu, Yongkang; Nie, Yuanyang; Xu, Peilun; Xia, Baixue; Tian, Fuzhou; Sun, Qun

    2015-01-01

    The prevalence of cholesterol gallstones has increased in recent years. Bacterial infection correlates with the formation of gallstones. We studied the composition and function of bacterial communities in cholesterol gallstones and bile from 22 cholesterol gallstone patients using culture-dependent and culture-independent methods. Altogether fourteen and eight bacterial genera were detected in cholesterol gallstones and bile, respectively. Pseudomonas spp. were the dominant bacteria in both cholesterol gallstones and bile. As judged by diversity indices, hierarchical clustering and principal component analysis, the bacterial communities in gallstones were different from those in bile. The gallstone microbiome was considered more stable than that of bile. The different microbial communities may be partially explained by differences in their habitats. We found that 30% of the culturable strains from cholesterol gallstones secreted β-glucuronidase and phospholipase A2. Pseudomonas aeruginosa strains showed the highest β-glucuronidase activity and produced the highest concentration of phospholipase A2, indicating that Ps. aeruginosa may be a major agent in the formation of cholesterol gallstones. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Differential iridoid production as revealed by a diversity panel of 84 cultivated and wild blueberry species.

    Directory of Open Access Journals (Sweden)

    Courtney P Leisner

    Full Text Available Cultivated blueberry (Vaccinium corymbosum, Vaccinium angustifolium, Vaccinium darrowii, and Vaccinium virgatum is an economically important fruit crop native to North America and a member of the Ericaceae family. Several species in the Ericaceae family including cranberry, lignonberry, bilberry, and neotropical blueberry species have been shown to produce iridoids, a class of pharmacologically important compounds present in over 15 plant families demonstrated to have a wide range of biological activities in humans including anti-cancer, anti-bacterial, and anti-inflammatory. While the antioxidant capacity of cultivated blueberry has been well studied, surveys of iridoid production in blueberry have been restricted to fruit of a very limited number of accessions of V. corymbosum, V. angustifolium and V. virgatum; none of these analyses have detected iridoids. To provide a broader survey of iridoid biosynthesis in cultivated blueberry, we constructed a panel of 84 accessions representing a wide range of cultivated market classes, as well as wild blueberry species, and surveyed these for the presence of iridoids. We identified the iridoid glycoside monotropein in fruits and leaves of all 13 wild Vaccinium species, yet only five of the 71 cultivars. Monotropein positive cultivars all had recent introgressions from wild species, suggesting that iridoid production can be targeted through breeding efforts that incorporate wild germplasm. A series of diverse developmental tissues was also surveyed in the diversity panel, demonstrating a wide range in iridoid content across tissues. Taken together, this data provides the foundation to dissect the molecular and genetic basis of iridoid production in blueberry.

  7. Redox-Stratified Bacterial Communities in Sediments Associated with Multiple Lucinid Bivalve Species: Implications for Symbiosis in Changing Coastal Habitats

    Science.gov (United States)

    Paterson, A. T.; Fortier, C. M.; Long, B.; Kokesh, B. S.; Lim, S. J.; Campbell, B. J.; Anderson, L. C.; Engel, A. S.

    2017-12-01

    Lucinids, chemosymbiotic marine bivalves, occupy strong redox gradient habitats, including the rhizosphere of coastal seagrass beds and mangrove forests in subtropical to tropical ecosystems. Lucinids and their sulfide-oxidizing gammaproteobacterial endosymbionts, which are acquired from the environment, provide a critical ecosystem service by removing toxic reduced sulfur compounds from the surrounding environment, and lucinids may be an important food source to economically valuable fisheries. The habitats of Phacoides pectinatus, Stewartia floridana, Codakia orbicularis, Ctena orbiculata, and Lucina pensylvanica lucinids in Florida and San Salvador in The Bahamas were evaluated in comprehensive malacological, microbiological, and geochemical surveys. Vegetation cover included different seagrass species or calcareous green macroalgae. All sites were variably affected by anthropogenic activities, as evidenced by visible prop scars in seagrass beds, grain size distributions atypical of low energy environments (i.e., artificial fill or dredge material from nearby channels), and high levels of pyrogenic hydrocarbon compounds in sediment indicative of urbanization impact. Where present, lucinid population densities frequently exceeded 2000 individuals per cubic meter, and were typically more abundant underlying seagrass compared to unvegetated, bare sand. Dissolved oxygen and sulfide levels varied from where lucinids were recovered. The sediment bacterial communities from classified 16S rRNA gene sequences indicated that the diversity of putative anaerobic groups increased with sediment depth, but putative aerobes, including of Gammaproteobacteria related to the lucinid endosymbionts, decreased with depth. Where multiple seagrass species co-occurred, retrieved bacterial community compositions correlated to overlying seagrass species, but diversity differed from bare sand patches, including among putative free-living endosymbiont groups. As such, continued sea

  8. Intestinal Microbiota and Species Diversity of Campylobacter and Helicobacter spp. in Migrating Shorebirds in Delaware Bay

    Science.gov (United States)

    Using rDNA sequencing analysis, we examined the bacterial diversity and the presence of opportunistic bacterial pathogens (i.e., Campylobacter and Helicobacter) in Red Knot (Calidris canutus, n=40), Ruddy Turnstone (Arenaria interpres, n=35), and Semipalmated Sandpiper (Calidris ...

  9. Spatial scaling of bacterial community diversity at shallow hydrothermal vents: a global comparison

    Science.gov (United States)

    Pop Ristova, P.; Hassenrueck, C.; Molari, M.; Fink, A.; Bühring, S. I.

    2016-02-01

    Marine shallow hydrothermal vents are extreme environments, often characterized by discharge of fluids with e.g. high temperatures, low pH, and laden with elements toxic to higher organisms. They occur at continental margins around the world's oceans, but represent fragmented, isolated habitats of locally small areal coverage. Microorganisms contribute the main biomass at shallow hydrothermal vent ecosystems and build the basis of the food chain by autotrophic fixation of carbon both via chemosynthesis and photosynthesis, occurring simultaneously. Despite their importance and unique capacity to adapt to these extreme environments, little is known about the spatial scales on which the alpha- and beta-diversity of microbial communities vary at shallow vents, and how the geochemical habitat heterogeneity influences shallow vent biodiversity. Here for the first time we investigated the spatial scaling of microbial biodiversity patterns and their interconnectivity at geochemically diverse shallow vents on a global scale. This study presents data on the comparison of bacterial community structures on large (> 1000 km) and small (0.1 - 100 m) spatial scales as derived from ARISA and Illumina sequencing. Despite the fragmented global distribution of shallow hydrothermal vents, similarity of vent bacterial communities decreased with geographic distance, confirming the ubiquity of distance-decay relationship. Moreover, at all investigated vents, pH was the main factor locally structuring these communities, while temperature influenced both the alpha- and beta-diversity.

  10. Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes.

    Science.gov (United States)

    Hu, Hang-Wei; Wang, Jun-Tao; Singh, Brajesh K; Liu, Yu-Rong; Chen, Yong-Liang; Zhang, Yu-Jing; He, Ji-Zheng

    2018-04-24

    Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected diverse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The diversity of ARGs was strongly and positively correlated with the diversity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

  11. Metagenomic survey of bacterial diversity in the atmosphere of Mexico City using different sampling methods.

    Science.gov (United States)

    Serrano-Silva, N; Calderón-Ezquerro, M C

    2018-04-01

    The identification of airborne bacteria has traditionally been performed by retrieval in culture media, but the bacterial diversity in the air is underestimated using this method because many bacteria are not readily cultured. Advances in DNA sequencing technology have produced a broad knowledge of genomics and metagenomics, which can greatly improve our ability to identify and study the diversity of airborne bacteria. However, researchers are facing several challenges, particularly the efficient retrieval of low-density microorganisms from the air and the lack of standardized protocols for sample collection and processing. In this study, we tested three methods for sampling bioaerosols - a Durham-type spore trap (Durham), a seven-day recording volumetric spore trap (HST), and a high-throughput 'Jet' spore and particle sampler (Jet) - and recovered metagenomic DNA for 16S rDNA sequencing. Samples were simultaneously collected with the three devices during one week, and the sequencing libraries were analyzed. A simple and efficient method for collecting bioaerosols and extracting good quality DNA for high-throughput sequencing was standardized. The Durham sampler collected preferentially Cyanobacteria, the HST Actinobacteria, Proteobacteria and Firmicutes, and the Jet mainly Proteobacteria and Firmicutes. The HST sampler collected the largest amount of airborne bacterial diversity. More experiments are necessary to select the right sampler, depending on study objectives, which may require monitoring and collecting specific airborne bacteria. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. OryzaGenome: Genome Diversity Database of Wild Oryza Species

    KAUST Repository

    Ohyanagi, Hajime

    2015-11-18

    The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/ scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

  13. Patterns and drivers of bacterial α- and β-diversity across vertical profiles from surface to subsurface sediments.

    Science.gov (United States)

    Luna, Gian Marco; Corinaldesi, Cinzia; Rastelli, Eugenio; Danovaro, Roberto

    2013-10-01

    We investigated the patterns and drivers of bacterial α- and β-diversity, along with viral and prokaryotic abundance and the carbon production rates, in marine surface and subsurface sediments (down to 1 m depth) in two habitats: vegetated sediments (seagrass meadow) and non-vegetated sediments. Prokaryotic abundance and production decreased with depth in the sediment, but cell-specific production rates and the virus-to-prokaryote ratio increased, highlighting unexpectedly high activity in the subsurface. The highest diversity was observed in vegetated sediments. Bacterial β-diversity between sediment horizons was high, and only a minor number of taxa was shared between surface and subsurface layers. Viruses significantly contributed to explain α- and β-diversity patterns. Despite potential limitations due to the only use of fingerprinting techniques, this study indicates that the coastal subsurface host highly active and diversified bacterial assemblages, that subsurface cells are more active than expected and that viruses promote β-diversity and stimulate bacterial metabolism in subsurface layers. The limited number of taxa shared between habitats, and between surface and subsurface sediment horizons, suggests that future investigations of the shallow subsurface will provide insights into the census of bacterial diversity, and the comprehension of the patterns and drivers of prokaryotic diversity in marine ecosystems. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  14. Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing

    Directory of Open Access Journals (Sweden)

    Wolcott Benjamin M

    2008-03-01

    Full Text Available Abstract Background Chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. These bacterial populations cooperate to promote their own survival and the chronic nature of the infection. Few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. The use of 3 separate16S-based molecular amplifications followed by pyrosequencing, shotgun Sanger sequencing, and denaturing gradient gel electrophoresis were utilized to survey the major populations of bacteria that occur in the pathogenic biofilms of three types of chronic wound types: diabetic foot ulcers (D, venous leg ulcers (V, and pressure ulcers (P. Results There are specific major populations of bacteria that were evident in the biofilms of all chronic wound types, including Staphylococcus, Pseudomonas, Peptoniphilus, Enterobacter, Stenotrophomonas, Finegoldia, and Serratia spp. Each of the wound types reveals marked differences in bacterial populations, such as pressure ulcers in which 62% of the populations were identified as obligate anaerobes. There were also populations of bacteria that were identified but not recognized as wound pathogens, such as Abiotrophia para-adiacens and Rhodopseudomonas spp. Results of molecular analyses were also compared to those obtained using traditional culture-based diagnostics. Only in one wound type did culture methods correctly identify the primary bacterial population indicating the need for improved diagnostic methods. Conclusion If clinicians can gain a better understanding of the wound's microbiota, it will give them a greater understanding of the wound's ecology and will allow them to better manage healing of the wound improving the prognosis of patients. This research highlights the necessity to begin evaluating, studying, and treating chronic wound pathogenic biofilms as multi-species entities in

  15. Survival of bacterial indicators and the functional diversity of native microbial communities in the Floridan aquifer system, south Florida

    Science.gov (United States)

    Lisle, John T.

    2014-01-01

    model than when exposed to groundwater from the APPZ (range: 0.540–0.684 h-1). The inactivation rates for the first phase of the models for P. aeruginosa were not significantly different between the UFA (range: 0.144–0.770 h-1) and APPZ (range: 0.159–0.772 h-1) aquifer zones. The inactivation rates for the second phase of the model for this P. aeruginosa were also similar between UFA (range: 0.003–0.008 h-1) and APPZ (0.004–0.005 h-1) zones, although significantly slower than the model’s first phase rates for this bacterial species. Geochemical data were used to determine which dissimilatory biogeochemical reactions were most likely to occur under the native conditions in the UFA and APPZ zones using thermodynamics principles to calculate free energy yields and other cell-related energetics data. The biogeochemical processes of acetotrophic and hydrogenotrophic sulfate reduction, methanogenesis and anaerobic oxidation of methane dominated in all six groundwater sites. A high throughput DNA microarray sequencing technology was used to characterize the diversity in the native aquifer bacterial communities (bacteria and archaea) and assign putative physiological capabilities to the members of those communities. The bacterial communities in both zones of the aquifer were shown to possess the capabilities for primary and secondary fermentation, acetogenesis, methanogenesis, anaerobic methane oxidation, syntrophy with methanogens, ammonification, and sulfate reduction. The data from this study provide the first determination of bacterial indicator survival during exposure to native geochemical conditions of the Floridan aquifer in south Florida. Additionally, the energetics and functional bacterial diversity characterizations are the first descriptions of native bacterial communities in this region of the Floridan aquifer and reveal how these communities persist under such extreme conditions. Collectively, these types of data can be used to develop and refine

  16. Identification of different bacterial species in biofilms using confocal Raman microscopy

    Science.gov (United States)

    Beier, Brooke D.; Quivey, Robert G.; Berger, Andrew J.

    2010-11-01

    Confocal Raman microspectroscopy is used to discriminate between different species of bacteria grown in biofilms. Tests are performed using two bacterial species, Streptococcus sanguinis and Streptococcus mutans, which are major components of oral plaque and of particular interest due to their association with healthy and cariogenic plaque, respectively. Dehydrated biofilms of these species are studied as a simplified model of dental plaque. A prediction model based on principal component analysis and logistic regression is calibrated using pure biofilms of each species and validated on pure biofilms grown months later, achieving 96% accuracy in prospective classification. When biofilms of the two species are partially mixed together, Raman-based identifications are achieved within ~2 μm of the boundaries between species with 97% accuracy. This combination of spatial resolution and predication accuracy should be suitable for forming images of species distributions within intact two-species biofilms.

  17. Biochemical fingerprinting of water coliform bacteria, a new method for measuring phenotypic diversity and for comparing different bacterial populations.

    Science.gov (United States)

    Kühn, I; Allestam, G; Stenström, T A; Möllby, R

    1991-01-01

    A simple, automated microplate system for biochemical characterization of water isolates can be used to obtain fingerprints of the bacterial flora from various water samples. Mathematical models for calculating the diversities and similarities between bacterial populations are described for such fingerprints. The diversity may give information on whether an indigenous or allochthonous flora is present, and the similarities between bacterial populations, as calculated by using a population similarity coefficient (Sp), may indicate contaminations between different water samples. The system was demonstrated on coliform bacterial populations from various water samples, with or without suspected intercontamination. For unrelated water samples, the Sps were close to 0, whereas repeated samples of the same source showed Sps of 0.64 to 0.74. The Sp values from several water samples were also clustered to form a dendrogram, thus indicating the relative similarities between the bacterial populations to confirm suspected common sources of pollution. PMID:1781680

  18. Phylogenetic diversity of dominant bacterial communities during bioremediation of crude oil-polluted soil

    Directory of Open Access Journals (Sweden)

    Eugene Thomas Cloete

    2011-08-01

    Full Text Available Bioremediation of hydrocarbon pollutants is advantageous owing to the cost-effectiveness of the technology and the ubiquity of hydrocarbon degrading microorganisms in the soil. Soil microbial diversity is affected by hydrocarbon perturbation thus selective enrichment of hydrocarbon utilizers occurs. Hydrocarbons interact with the soil matrix and soil microorganisms determining the fate of the contaminants relative to their chemical nature and microbial degradative capabilities respectively. Bacterial dynamics in crude oil-polluted soil microcosms undergoing bioremediation were investigated over a 42-day period. Four out of the five microcosms containing 4kg of pristine soil each were contaminated with 4% Arabian light crude oil. Three microcosms were amended with either 25g of NPK fertilizer, calcium ammonium nitrate or poultry droppings respectively while the fourth designated oil-contaminated control was unamended. The fifth microcosm had only pristine soil and was set up to ascertain indigenous bacterial community structure pre-contamination. Biostimulated soils were periodically tilled and watered. Hydrocarbon degradation was measured throughout the experimental period by gas chromatography. Gas chromatographic tracing of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second (day 14 till the sixth (day 42 week after contamination whereas no significant reduction in hydrocarbon peaks was seen in the oil contaminated control soil throughout the 6-week experimental period. Molecular fingerprints of bacterial communities involved in aerobic biodegradation of crude oil hydrocarbons in biostimulated soils and controls were generated with DGGE using PCR-amplification of 16S rRNA gene obtained from extracted total soil community DNA. DGGE fingerprints demonstrated that NPK, calcium ammonium nitrate and poultry droppings selected different bacterial populations during the active phase of oil

  19. Diversity and utilization of bamboo species in Tigawasa Village, Bali

    Directory of Open Access Journals (Sweden)

    IDA BAGUS KETUT ARINASA

    2005-01-01

    Full Text Available Tigawasa is one of the famous traditional villages as a center of bamboo handicraft in Buleleng regency-Bali. As a center of bamboo handicraft its have been wrestled since centuries. Their peoples have done traditionally bamboo conservation surrounding their house and garden too. The marginal area, river flow area and stiff slope that are outskirts of village become to focus of bamboo conservation by their peoples, too. This research conducted at Tigawasa village in June 2003 by stripe and interview methods. Two kilometers stripe length by 50 meters width; follow the direction north south of the river was investigated. To know the utilization of kind of bamboo and their product conducted by interview to craftsman and community figure. The result of inventory knew about four genus consist of 19 species planted in this village. To know those bamboo species will be presented their key of determination. The genus of Gigantochloa and Schizostachyum to dominate of their species, and have many uses of it’s, also. Not less than 54 kind of bamboos handicraft product was produced in this village. The diversity of bamboos handicraft product, develop according progress of the technology and demand of period. Many of new products composed and use of color or paint develop to produce varieties of fixed product. Two-kind of product that is traditional boxes (“sokasi” handicraft and woven bamboo (“bedeg” to become this village famous at Bali, even though in foreign countries Energetic development of bamboos home industry to come to decrease stock of raw materials. About two trucks supply from east Java regularly to anticipation of decrease local stock of raw materials every week.

  20. [Bacterial diversity in the oral cavity of adolescents with different caries susceptibilities].

    Science.gov (United States)

    Yangyang, Zhang; Jinzhi, He; Xin, Xu; Xuedong, Zhou

    2015-12-01

    To analyze the differences between the bacterial diversities in the saliva of caries-free and caries-susceptible adolescents through polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE). Twenty adolescent subjects aged 12-18 years were recruited and subdivided into two groups: caries-free adolescents (n = 10) and caries-susceptible adolescents (n = 10). Saliva samples were collected. Total DNA was isolated directly from each sample. A portion of the 16S rRNA gene locus was PCR-amplified by using universal primers. Microbial diversity was analyzed through PCR-DGGE. Analyzing the DGGE profile, we found that the composition of the saliva microbiome exhibited great intra-individual differences; the average band numbers of the caries-free adolescent group and the caries-susceptible adolescent group were 32.5 ± 3.7 and 27.3 ± 3.4, respectively. The differences between the groups were statistically significant (P = 0.008). Shannon-Wiener's indexes of the caries-susceptible adolescent group and the caries-free adolescent group were 2.5 ± 0.2 and 2.6 ± 0.2, respectively, but the differences between the groups were not significant (P = 0.405). Clustering analysis results suggested that most of the samples in the same group clustered together; this observation showed a high community structure similarity. The microbial diversity and complexity of bacteria in saliva are significantly higher in caries-free adolescents than in caries-susceptible adolescents. During caries development, bacterial diversity in the saliva likely decreases.

  1. Long term repeated fire disturbance alters soil bacterial diversity but not the abundance in an Australian wet sclerophyll forest.

    Science.gov (United States)

    Shen, Ju-pei; Chen, C R; Lewis, Tom

    2016-01-20

    Effects of fire on biogeochemical cycling in terrestrial ecosystem are widely acknowledged, while few studies have focused on the bacterial community under the disturbance of long-term frequent prescribed fire. In this study, three treatments (burning every two years (B2), burning every four years (B4) and no burning (B0)) were applied for 38 years in an Australian wet sclerophyll forest. Results showed that bacterial alpha diversity (i.e. bacterial OTU) in the top soil (0-10 cm) was significantly higher in the B2 treatment compared with the B0 and B4 treatments. Non-metric multidimensional analysis (NMDS) of bacterial community showed clear separation of the soil bacterial community structure among different fire frequency regimes and between the depths. Different frequency fire did not have a substantial effect on bacterial composition at phylum level or bacterial 16S rRNA gene abundance. Soil pH and C:N ratio were the major drivers for bacterial community structure in the most frequent fire treatment (B2), while other factors (EC, DOC, DON, MBC, NH4(+), TC and TN) were significant in the less frequent burning and no burning treatments (B4 and B0). This study suggested that burning had a dramatic impact on bacterial diversity but not abundance with more frequent fire.

  2. Effect of species, breed, and age on bacterial load in bovine and bubaline semen

    Science.gov (United States)

    Sannat, Chandrahas; Nair, Ajit; Sahu, S. B.; Sahasrabudhe, S. A.; Kumar, Ashish; Gupta, Amit Kumar; Shende, R. K.

    2015-01-01

    Aim: The present study was conducted to investigate the effect of species, breed and age on bacterial load in fresh and frozen semen of Cattle and Buffalo bull. Materials and Methods: Present study covered 56 cow and 10 buffalo bulls stationed at Central Semen Station Anjora, Durg (Chhattisgarh). Impact of breeds on bacterial load in semen was assessed using six breeds of cattle viz. Sahiwal, Gir, Red Sindhi, Tharparkar, Jersey and Holstein Friesian (HF) cross. Cow bulls were categorized into four different groups based on their age ( 6 years) to study variation among age groups. Bacterial load was measured in fresh and frozen semen samples from these bulls using the standard plate count (SPC) method and count was expressed as colony forming unit (CFU) per ml of semen. Results: Higher bacterial load was reported in fresh (2.36 × 104 ± 1943 CFU/ml) and frozen (1.00 × 10 ± 90 CFU/ml) semen of cow bulls as compared to buffalo bulls (1.95 × 104 ± 2882 and 7.75 × 102 ± 160 CFU/ml in fresh and frozen semen, respectively). Jersey bull showed significantly higher bacterial count (p semen followed by HF cross, Sahiwal, Gir, Red Sindhi and Tharparkar bull. Bulls aged semen. Although a minor variation was reported between species and among age groups, no significant differences were measured. Conclusion: Bacterial load in semen did not differ significantly between species and age groups; however significant variation was reported among different breeds. Bulls of Jersey breed showed significantly higher bacterial load in semen as compared to the crossbred and indigenous bull. PMID:27047115

  3. Microplastics as a vector for the transport of the bacterial fish pathogen species Aeromonas salmonicida.

    Science.gov (United States)

    Viršek, Manca Kovač; Lovšin, Marija Nika; Koren, Špela; Kržan, Andrej; Peterlin, Monika

    2017-12-15

    Microplastics is widespread in the marine environment where it can cause numerous negative effects. It can provide space for the growth of organisms and serves as a vector for the long distance transfer of marine microorganisms. In this study, we examined the sea surface concentrations of microplastics in the North Adriatic and characterized bacterial communities living on the microplastics. DNA from microplastics particles was isolated by three different methods, followed by PCR amplification of 16S rDNA, clone libraries preparation and phylogenetic analysis. 28 bacterial species were identified on the microplastics particles including Aeromonas spp. and hydrocarbon-degrading bacterial species. Based on the 16S rDNA sequences the pathogenic fish bacteria Aeromonas salmonicida was identified for the first time on microplastics. Because A. salmonicida is responsible for illnesses in fish, it is crucial to get answers if and how microplastics pollution is responsible for spreading of diseases. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Bacterial Diversity Associated with Cinachyra cavernosa and Haliclona pigmentifera, Cohabiting Sponges in the Coral Reef Ecosystem of Gulf of Mannar, Southeast Coast of India.

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    C Jasmin

    Full Text Available Sponges are abundant, diverse and functionally important organisms of coral reef ecosystems. Sponge-associated microorganisms have been receiving greater attention because of their significant contribution to sponge biomass, biogeochemical cycles and biotechnological potentials. However, our understanding of the sponge microbiome is limited to a few species of sponges from restricted geographical locations. Here, we report for the first time the bacterial diversity of two cohabiting sponges, viz. Cinachyra cavernosa and Haliclona pigmentifera, as well as that in the ambient water from the coral reef ecosystems of the Gulf of Mannar, located along the southeast coast of India. Two hundred and fifty two clones in the 16S rRNA gene library of these sponges were grouped into eight distinct phyla, of which four belonged to the core group that are associated only with sponges. Phylogenetic analysis of the core bacteria showed close affinity to other sponge-associated bacteria from different geographical locations. γ-Proteobacteria, Chloroflexi, Planctomycetes and Deferribacter were the core groups in C. cavernosa while β and δ-Proteobacteria performed this role in H. pigmentifera. We observed greater OTU diversity for C. cavernosa (Hǀ 2.07 compared to H. pigmentifera (Hǀ 1.97. UniFrac analysis confirmed the difference in bacterial diversity of the two sponge species and also between the sponges and the reef water (p<0.001. The results of our study restate the existence of a host driven force in shaping the sponge microbiome.

  5. “Lachnoclostridium touaregense,” a new bacterial species isolated from the human gut microbiota

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    M. Tidjani Alou

    2016-11-01

    Full Text Available We report the main characteristics of “Lachnoclostridium touaregense” strain Marseille-P2415T (= CSUR P2415 = DSM 102219, a new bacterial species isolated from the gut microbiota of a healthy young girl from Niger.

  6. ‘Tidjanibacter massiliensis’ gen. nov., sp. nov., a new bacterial species isolated from human colon

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    M. Mailhe

    2017-05-01

    Full Text Available We report the summary of main characteristics of Tidjanibacter massiliensis strain Marseille-P3084T, a new bacterial species isolated from the liquid sample of the colon of a patient with a history of irritable bowel syndrome.

  7. Degradation of lucerne stem cell walls by five rumen bacterial species

    NARCIS (Netherlands)

    Jung, H.G.; Engels, F.M.; Weimer, P.J.

    2004-01-01

    The rumen bacterial strains Butyrivibrio fibrisolvens H17c, Fibrobacter succinogenes S85, Lachnospira multiparus 40, Ruminococcus albus 7 and R. flavefaciens FD-1 were compared individually and as a five-species mixture with a rumen inoculum for their ability to degrade lucerne (Medicago sativa L.)

  8. Diversity of bacterial communities along a petroleum contamination gradient in desert soils.

    Science.gov (United States)

    Abed, Raeid M M; Al-Kindi, Sumaiya; Al-Kharusi, Samiha

    2015-01-01

    Microbial communities in oil-polluted desert soils have been rarely studied compared to their counterparts from freshwater and marine environments. We investigated bacterial diversity and changes therein in five desert soils exposed to different levels of oil pollution. Automated rRNA intergenic spacer (ARISA) analysis profiles showed that the bacterial communities of the five soils were profoundly different (analysis of similarities (ANOSIM), R = 0.45, P pollution levels. Multivariate analyses of ARISA profiles revealed that the microbial communities in the S soil, which contains the highest level of contamination, were different from the other soils and formed a completely separate cluster. A total of 16,657 ribosomal sequences were obtained, with 42-89 % of these sequences belonging to the phylum Proteobacteria. While sequences belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, and Actinobacteria were encountered in all soils, sequences belonging to anaerobic bacteria from the classes Deltaproteobacteria, Clostridia, and Anaerolineae were only detected in the S soil. Sequences belonging to the genus Terriglobus of the class Acidobacteria were only detected in the B3 soil with the lowest level of contamination. Redundancy analysis (RDA) showed that oil contamination level was the most determinant factor that explained variations in the microbial communities. We conclude that the exposure to different levels of oil contamination exerts a strong selective pressure on bacterial communities and that desert soils are rich in aerobic and anaerobic bacteria that could potentially contribute to the degradation of hydrocarbons.

  9. Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

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    Giuseppe D’Auria

    2018-01-01

    Full Text Available New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300–500 mg L-1 H2S and <0.1 mg L-1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample

  10. Bioprospecting saline gradient of a Wildlife Sanctuary for bacterial diversity and antimicrobial activities.

    Science.gov (United States)

    DeLuca, Mara; King, Riley; Morsy, Mustafa

    2017-08-11

    Antibiotic-resistant bacteria are becoming a global crisis, causing death of thousands of people and significant economic impact. The discovery of novel antibiotics is crucial to saving lives and reducing healthcare costs. To address the antibiotic-resistant crisis, in collaboration the Small World Initiative, which aims to crowdsource novel antibiotic discovery, this study aimed to identify antimicrobial producing bacteria and bacterial diversity in the soil of the Stimpson Wildlife Sanctuary, an inland area with a soil salt gradient. Approximately 4500 bacterial colonies were screened for antimicrobial activity and roughly 100 bacteria were identified as antimicrobial producers, which belong to Entrococcaceae (74%), Yersiniaceae (19%), and unidentified families (7%). Several bacterial isolates showed production of broad spectrum inhibitory compounds, while others were more specific to certain pathogens. The data obtained from the current study provide a resource for further characterization of the soil bacteria with antimicrobial activity, with an aim to discover novel ones. The study showed no correlation between soil salt level and the presence of bacteria with antimicrobial activities. However, most of the identified antimicrobial producing bacteria do not belong to actinomycetes, the most common phyla of antibiotic producing bacteria and this could potentially lead to the discovery of novel antibiotics.

  11. Quantifying species diversity with a DNA barcoding-based method: Tibetan moth species (Noctuidae on the Qinghai-Tibetan Plateau.

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    Qian Jin

    Full Text Available With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of 9.45±2.08%, which is about four times larger than the mean intraspecific distance (1.85±3.20%. Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau.

  12. Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau

    Science.gov (United States)

    Jin, Qian; Han, Huilin; Hu, XiMin; Li, XinHai; Zhu, ChaoDong; Ho, Simon Y. W.; Ward, Robert D.; Zhang, Ai-bing

    2013-01-01

    With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of , which is about four times larger than the mean intraspecific distance (). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau. PMID:23741330

  13. Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile

    Science.gov (United States)

    Neilson, Julia W.; Quade, Jay; Ortiz, Marianyoly; Nelson, William M.; Legatzki, Antje; Tian, Fei; LaComb, Michelle; Betancourt, Julio L.; Wing, Rod A.; Soderlund, Carol A.; Maier, Raina M.

    2012-01-01

    Nearly half the earth's surface is occupied by dryland ecosystems, regions susceptible to reduced states of biological productivity caused by climate fluctuations. Of these regions, arid zones located at the interface between vegetated semiarid regions and biologically unproductive hyperarid zones are considered most vulnerable. The objective of this study was to conduct a deep diversity analysis of bacterial communities in unvegetated arid soils of the Atacama Desert, to characterize community structure and infer the functional potential of these communities based on observed phylogenetic associations. A 454-pyrotag analysis was conducted of three unvegetated arid sites located at the hyperarid-arid margin. The analysis revealed communities with unique bacterial diversity marked by high abundances of novel Actinobacteria and Chloroflexi and low levels of Acidobacteria and Proteobacteria, phyla that are dominant in many biomes. A 16S rRNA gene library of one site revealed the presence of clones with phylogenetic associations to chemoautotrophic taxa able to obtain energy through oxidation of nitrite, carbon monoxide, iron, or sulfur. Thus, soils at the hyperarid margin were found to harbor a wealth of novel bacteria and to support potentially viable communities with phylogenetic associations to non-phototrophic primary producers and bacteria capable of biogeochemical cycling.

  14. Diversity of Extremely Halophilic Archaeal and Bacterial Communities from Commercial Salts.

    Science.gov (United States)

    Gibtan, Ashagrie; Park, Kyounghee; Woo, Mingyeong; Shin, Jung-Kue; Lee, Dong-Woo; Sohn, Jae Hak; Song, Minjung; Roh, Seong Woon; Lee, Sang-Jae; Lee, Han-Seung

    2017-01-01

    Salting is one of the oldest food preservation techniques. However, salt is also the source of living halophilic microorganisms that may affect human health. In order to determine the microbial communities of commercial salts, an investigation were done using amplicon sequencing approach in four commercial salts: Ethiopian Afdera salt (EAS), Ethiopian rock salt (ERS), Korean Jangpan salt (KJS), and Korean Topan salt (KTS). Using domain-specific primers, a region of the 16S rRNA gene was amplified and sequenced using a Roche 454 instrument. The results indicated that these microbial communities contained 48.22-61.4% Bacteria, 37.72-51.26% Archaea, 0.51-0.86% Eukarya, and 0.005-0.009% unclassified reads. Among bacteria, the communities in these salts were dominated by the phyla Proteobacteria, Bacteroidetes, Actinobacteria , and Firmicutes . Of the archaea, 91.58% belonged to the class Halobacteria , whereas the remaining 7.58, 0.83, and 0.01% were Nanoarchaea, Methanobacteria , and Thermococci , respectively. This comparison of microbial diversity in salts from two countries showed the presence of many archaeal and bacterial genera that occurred in salt samples from one country but not the other. The bacterial genera Enterobacter and Halovibrio were found only in Korean and Ethiopian salts, respectively. This study indicated the occurrence and diversity of halophilic bacteria and archaea in commercial salts that could be important in the gastrointestinal tract after ingestion.

  15. Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile.

    Science.gov (United States)

    Neilson, Julia W; Quade, Jay; Ortiz, Marianyoly; Nelson, William M; Legatzki, Antje; Tian, Fei; LaComb, Michelle; Betancourt, Julio L; Wing, Rod A; Soderlund, Carol A; Maier, Raina M

    2012-05-01

    Nearly half the earth's surface is occupied by dryland ecosystems, regions susceptible to reduced states of biological productivity caused by climate fluctuations. Of these regions, arid zones located at the interface between vegetated semiarid regions and biologically unproductive hyperarid zones are considered most vulnerable. The objective of this study was to conduct a deep diversity analysis of bacterial communities in unvegetated arid soils of the Atacama Desert, to characterize community structure and infer the functional potential of these communities based on observed phylogenetic associations. A 454-pyrotag analysis was conducted of three unvegetated arid sites located at the hyperarid-arid margin. The analysis revealed communities with unique bacterial diversity marked by high abundances of novel Actinobacteria and Chloroflexi and low levels of Acidobacteria and Proteobacteria, phyla that are dominant in many biomes. A 16S rRNA gene library of one site revealed the presence of clones with phylogenetic associations to chemoautotrophic taxa able to obtain energy through oxidation of nitrite, carbon monoxide, iron, or sulfur. Thus, soils at the hyperarid margin were found to harbor a wealth of novel bacteria and to support potentially viable communities with phylogenetic associations to non-phototrophic primary producers and bacteria capable of biogeochemical cycling.

  16. Endophytic bacterial diversity in the phyllosphere of Amazon Paullinia cupana associated with asymptomatic and symptomatic anthracnose.

    Science.gov (United States)

    Bogas, Andréa Cristina; Ferreira, Almir José; Araújo, Welington Luiz; Astolfi-Filho, Spartaco; Kitajima, Elliot Watanabe; Lacava, Paulo Teixeira; Azevedo, João Lúcio

    2015-01-01

    Endophytes colonize an ecological niche similar to that of phytopathogens, which make them candidate for disease suppression. Anthracnose is a disease caused by Colletotrichum spp., a phytopathogen that can infect guarana (Paullinia cupana), an important commercial crop in the Brazilian Amazon. We investigated the diversity of endophytic bacteria inhabiting the phyllosphere of asymptomatic and symptomatic anthracnose guarana plants. The PCR-denaturation gradient gel electrophoresis (PCR-DGGE) fingerprints revealed differences in the structure of the evaluated communities. Detailed analysis of endophytic bacteria composition using culture-dependent and 16S rRNA clone libraries revealed the presence of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria phyla. Firmicutes comprised the majority of isolates in asymptomatic plants (2.40E(-4)). However, cloning and sequencing of 16S rRNA revealed differences at the genus level for Neisseria (1.4E(-4)), Haemophilus (2.1E(-3)) and Arsenophonus (3.6E(-5)) in asymptomatic plants, Aquicella (3.5E(-3)) in symptomatic anthracnose plants, and Pseudomonas (1.1E(-3)), which was mainly identified in asymptomatic plants. In cross-comparisons of the endophytic bacterial communities as a whole, symptomatic anthracnose plants contained higher diversity, as reflected in the Shannon-Weaver and Simpson indices estimation (P anthracnose can restructure endophytic bacterial communities by selecting certain strains in the phyllosphere of P. cupana. The understanding of these interactions is important for the development of strategies of biocontrol for Colletotrichum.

  17. Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: diversity and seasonal variability.

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    James R White

    Full Text Available BACKGROUND: Marine sponge species are of significant interest to many scientific fields including marine ecology, conservation biology, genetics, host-microbe symbiosis and pharmacology. One of the most intriguing aspects of the sponge "holobiont" system is the unique physiology, interaction with microbes from the marine environment and the development of a complex commensal microbial community. However, intraspecific variability and temporal stability of sponge-associated bacterial symbionts remain relatively unknown. METHODOLOGY/PRINCIPAL FINDINGS: We have characterized the bacterial symbiont community biodiversity of seven different individuals of the Caribbean reef sponge Axinella corrugata, from two different Florida reef locations during variable seasons using multiplex 454 pyrosequencing of 16 S rRNA amplicons. Over 265,512 high-quality 16 S rRNA sequences were generated and analyzed. Utilizing versatile bioinformatics methods and analytical software such as the QIIME and CloVR packages, we have identified 9,444 distinct bacterial operational taxonomic units (OTUs. Approximately 65,550 rRNA sequences (24% could not be matched to bacteria at the class level, and may therefore represent novel taxa. Differentially abundant classes between seasonal Axinella communities included Gammaproteobacteria, Flavobacteria, Alphaproteobacteria, Cyanobacteria, Acidobacter and Nitrospira. Comparisons with a proximal outgroup sponge species (Amphimedon compressa, and the growing sponge symbiont literature, indicate that this study has identified approximately 330 A. corrugata-specific symbiotic OTUs, many of which are related to the sulfur-oxidizing Ectothiorhodospiraceae. This family appeared exclusively within A. corrugata, comprising >34.5% of all sequenced amplicons. Other A. corrugata symbionts such as Deltaproteobacteria, Bdellovibrio, and Thiocystis among many others are described. CONCLUSIONS/SIGNIFICANCE: Slight shifts in several bacterial taxa

  18. The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

    Science.gov (United States)

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between

  19. Woody species diversity in forest plantations in a mountainous region of Beijing, China: effects of sampling scale and species selection.

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    Yuxin Zhang

    Full Text Available The role of forest plantations in biodiversity conservation has gained more attention in recent years. However, most work on evaluating the diversity of forest plantations focuses only on one spatial scale; thus, we examined the effects of sampling scale on diversity in forest plantations. We designed a hierarchical sampling strategy to collect data on woody species diversity in planted pine (Pinus tabuliformis Carr., planted larch (Larix principis-rupprechtii Mayr., and natural secondary deciduous broadleaf forests in a mountainous region of Beijing, China. Additive diversity partition analysis showed that, compared to natural forests, the planted pine forests had a different woody species diversity partitioning pattern at multi-scales (except the Simpson diversity in the regeneration layer, while the larch plantations did not show multi-scale diversity partitioning patterns that were obviously different from those in the natural secondary broadleaf forest. Compare to the natural secondary broadleaf forests, the effects of planted pine forests on woody species diversity are dependent on the sampling scale and layers selected for analysis. Diversity in the planted larch forest, however, was not significantly different from that in the natural forest for all diversity components at all sampling levels. Our work demonstrated that the species selected for afforestation and the sampling scales selected for data analysis alter the conclusions on the levels of diversity supported by plantations. We suggest that a wide range of scales should be considered in the evaluation of the role of forest plantations on biodiversity conservation.

  20. Effect of semi-permeable cover system on the bacterial diversity during sewage sludge composting.

    Science.gov (United States)

    Robledo-Mahón, Tatiana; Aranda, Elisabet; Pesciaroli, Chiara; Rodríguez-Calvo, Alfonso; Silva-Castro, Gloria Andrea; González-López, Jesús; Calvo, Concepción

    2018-06-01

    Sewage sludge composting is a profitable process economically viable and environmentally friendly. In despite of there are several kind of composting types, the use of combined system of semipermeable cover film and aeration air-floor is widely developed at industrial scale. However, the knowledge of the linkages between microbial communities structure, enzyme activities and physico-chemical factors under these conditions it has been poorly explored. Thus, the aim of this study was to investigate the bacterial dynamic and community structure using next generation sequencing coupled to analyses of microbial enzymatic activity and culturable dependent techniques in a full-scale real composting plant. Sewage sludge composting process was conducted using a semi-permeable Gore-tex cover, in combination with an air-insufflation system. The highest values of enzymatic activities such as dehydrogenase, protease and arylsulphatase were detected in the first 5 days of composting; suggesting that during this period of time a greater degrading activity of organic matter took place. Culturable bacteria identified were in agreement with the bacteria found by massive sequencing technologies. The greatest bacterial diversity was detected between days 15 and 30, with Actinomycetales and Bacillales being the predominant orders at the beginning and end of the process. Bacillus was the most representative genus during all the process. A strong correlation between abiotic factors as total organic content and organic matter and enzymatic activities such as dehydrogenase, alkaline phosphatase, and ß-glucosidase activity was found. Bacterial diversity was strongly influenced by the stage of the process, community-structure change was concomitant with a temperature rise, rendering favorable conditions to stimulate microbial activity and facilitate the change in the microbial community linked to the degradation process. Moreover, results obtained confirmed that the use of semipermeable

  1. Tree structural and species diversities in Okwangwo Forest, Cross ...

    African Journals Online (AJOL)

    Tree species were grouped into abundance classes. A total of 125 tree species belonging to 36 families and 96 genera were recorded in the area with Margaleffs index of species richness of 2.2754. Most (99) of the tree species encountered were threatened/endangered, 23 species were rare with only 3 tree species ...

  2. Multilayer Approach for Characterization of Bacterial Diversity in a Marginal Sea: From Surface to Seabed

    Science.gov (United States)

    Ivana, Babic; Maja, Mucko; Ivica, Vilibic; Hrvoje, Mihanovic; Reffaella, Casotti; Zrinka, Ljubesic; Ivona, Cetinic; Cecilia, Balestra; Ines, Petric; Suncica, Bosak; hide

    2018-01-01

    Bacteria are the most important microorganisms in the world oceans, accounting for up to 75% of the total biomass. They are responsible for fundamental biogeochemical processes and therefore often used as ecological indicators. In this study, bacteria were quantified by flow cytometry and their diversity assessed by High Throughput Sequencing (HTS) in the southern Adriatic Sea. The most abundant bacterial groups were also quantified by qPCR. The samples were collected from the surface to the seabed over a total of 16 different depths at four stations during the late winter BIOTA (BIO-Tracing Adriatic water masses) cruise conducted in March 2016. The investigated area showed unusual water mass properties and was characterized by a shallow mixed layer, which differed from the usual winter convection conditions, typical of middle-altitude ecosystems and important for the seasonal picoplankton dynamics of this area. Heterotrophic bacteria were separated into HNA (relative High Nucleic Acid content) and LNA (Low Nucleic Acid content) subpopulations with abundances up to 1.8×10(exp 5) and 8.8×10(exp 5) cells/mL, respectively. HNA dominated at offshore stations reaching their maximum at depths below the euphotic zone. The bacterial community was dominated by Alphaproteobacteria, accounting for greater than 40% of the total sequence reads and were mainly represented by the SAR11 clade (90.84%), followed by Marinimicrobia (18% of the total sequence reads), mainly represented by clade SAR406 (8.44%). Distinctive bacterial groups were found in the euphotic layer (Bacteroidetes and Actinobacteria) and aphotic layer samples (Deltaproteobacteria, Marinimicrobia, Chloroflexi, Acidobacteria and Planctomycetes). Results of the qPCR analyses further confirmed HTS results with highest abundances obtained for Alphaproteobacteria, followed by Gammaproteobacteria and Bacteroidetes. The adopted multiple approach, combining different molecular tools, critically supported by optics and

  3. Body size and measurement of species diversity in large grazing mammals

    NARCIS (Netherlands)

    Oindo, B.O.

    2002-01-01

    Species are by definition different from each other. This fact favours ranking rather than additive indices. However, ecologists have measured species diversity in terms of species richness, or by combining species richness with the relative abundance of species within an area. Both methods raise

  4. Assessment of bacterial diversity in Hyalomma aegyptium, H. marginatum and H. excavatum ticks through tag-encoded pyrosequencing.

    Science.gov (United States)

    Keskin, Adem; Bursali, Ahmet; Snow, David E; Dowd, Scot E; Tekin, Saban

    2017-12-01

    Ticks are among the most significant human-biting ectoparasites and they play a major role in transmission of many pathogenic agents to humans. In the present study, three species of Hyalomma ticks, Hyalomma aegyptium, H. marginatum and H. excavatum, were examined for the presence of zoonotic bacteria, both male and female ticks alike. Examination of microbial diversity with tag-encoded pyrosequencing indicates that H. marginatum and H. excavatum were more diversity rich than H. aegyptium. Although numerous pathogenic and non-pathogenic bacterial genera were detected, including Acidovorax, Bacillus, Bacteroides, Bdellovibrio, Clostridium, Curvibacter, Escherichia, Flavobacterium, Limnohabitans, Paenibacillus, Ralstonia, Sarcina, Sediminibacterium, Segetibacter Stenotrophomonas and Variovorax, the predominant zoonotic bacteria represented in these ticks were genera Borrelia, Francisella, and Rickettsia. To the authors' knowledge, this work represents the first detection of Yersinia enterocolitica in the tick H. excavatum, raising questions regarding the vector competency of this tick, as well as associations of different disease representations perhaps through previously unforeseen routes of pathogen introduction. Likewise, similar questions are related to the presence of Legionella pneumophila in one H. excavatum sample.

  5. Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea

    Science.gov (United States)

    Zhang, Yao; Zhao, Zihao; Dai, Minhan; Jiao, Nianzhi; Herndl, Gerhard J

    2014-01-01

    To test the hypothesis that different drivers shape the diversity and biogeography of the total and active bacterial community, we examined the bacterial community composition along two transects, one from the inner Pearl River estuary to the open waters of the South China Sea (SCS) and the other from the Luzon Strait to the SCS basin, using 454 pyrosequencing of the 16S rRNA and 16S rRNA gene (V1-3 regions) and thereby characterizing the active and total bacterial community, respectively. The diversity and biogeographic patterns differed substantially between the active and total bacterial communities. Although the composition of both the total and active bacterial community was strongly correlated with environmental factors and weakly correlated with geographic distance, the active bacterial community displayed higher environmental sensitivity than the total community and particularly a greater distance effect largely caused by the active assemblage from deep waters. The 16S rRNA vs. rDNA relationships indicated that the active bacteria were low in relative abundance in the SCS. This might be due to a high competition between active bacterial taxa as indicated by our community network models. Based on these analyses, we speculate that high competition could cause some dispersal limitation of the active bacterial community resulting in a distinct distance-decay relationship. Altogether, our results indicated that the biogeographic distribution of bacteria in the SCS is the result of both environmental control and distance decay. PMID:24684298

  6. Isolation of Geobacter species from diverse sedimentary environments

    Science.gov (United States)

    Coaxes, J.D.; Phillips, E.J.P.; Lonergan, D.J.; Jenter, H.; Lovley, D.R.

    1996-01-01

    In an attempt to better understand the microorganisms responsible for Fe(III) reduction in sedimentary environments, Fe(III)-reducing microorganisms were enriched for and isolated from freshwater aquatic sediments, a pristine deep aquifer, and a petroleum-contaminated shallow aquifer. Enrichments were initiated with acetate or toluene as the electron donor and Fe(III) as the electron acceptor. Isolations were made with acetate or benzoate. Five new strains which could obtain energy for growth by dissimilatory Fe(III) reduction were isolated. All five isolates are gram- negative strict anaerobes which grow with acetate as the electron donor and Fe(III) as the electron acceptor. Analysis of the 16S rRNA sequence of the isolated organisms demonstrated that they all belonged to the genus Geobacter in the delta subdivision of the Proteobacteria. Unlike the type strain, Geobacter metallireducens, three of the five isolates could use H2 as an electron donor fur Fe(III) reduction. The deep subsurface isolate is the first Fe(III) reducer shown to completely oxidize lactate to carbon dioxide, while one of the freshwater sediment isolates is only the second Fe(III) reducer known that can oxidize toluene. The isolation of these organisms demonstrates that Geobacter species are widely distributed in a diversity of sedimentary environments in which Fe(III) reduction is an important process.

  7. Positive and negative associations between bacterial species in dental root canals.

    Science.gov (United States)

    Gomes, B P; Drucker, D B; Lilley, J D

    1994-01-01

    Significant associations have been previously reported between certain pairs of bacterial species isolated from human dental root canals. The aim of this study was to examine microbiologically a more extensive series of cases, with particular reference to obligate anaerobes which accounted for 64% of total isolations. A total of 65 different species was isolated and individual root canals yielded a maximum of eleven bacterial species. Highly significant positive associations (p spp. and Prevotella spp., between Peptostreptococcus spp. and P. melaninogenica, between P. micros and Prevotella spp., P. micros and P. melaninogenica and between Prevotella spp. and Eubacterium spp., all with an ODDS ratio of > 9.0. In contrast, negative and highly significant associations (p spp., B. gracilis/F. nucleatum and between B. gracilis/Fusobacterium spp.; all with an ODDS ratio of < 0.5. Some previously published associations were confirmed and some new associations were found, while some negative associations became apparent.

  8. Diversity within diversity: Parasite species richness in poison frogs assessed by transcriptomics.

    Science.gov (United States)

    Santos, Juan C; Tarvin, Rebecca D; O'Connell, Lauren A; Blackburn, David C; Coloma, Luis A

    2018-08-01

    Symbionts (e.g., endoparasites and commensals) play an integral role in their host's ecology, yet in many cases their diversity is likely underestimated. Although endoparasites are traditionally characterized using morphology, sequences of conserved genes, and shotgun metagenomics, host transcriptomes constitute an underused resource to identify these organisms' diversity. By isolating non-host transcripts from host transcriptomes, individual host tissues can now simultaneously reveal their endoparasite species richness (i.e., number of different taxa) and provide insights into parasite gene expression. These approaches can be used in host taxa whose endoparasites are mostly unknown, such as those of tropical amphibians. Here, we focus on the poison frogs (Dendrobatidae) as hosts, which are a Neotropical clade known for their bright coloration and defensive alkaloids. These toxins are an effective protection against vertebrate predators (e.g., snakes and birds), bacteria, and skin-biting ectoparasites (e.g., mosquitoes); however, little is known about their deterrence against eukaryotic endoparasites. With de novo transcriptomes of dendrobatids, we developed a bioinformatics pipeline for endoparasite identification that uses host annotated RNA-seq data and set of a priori parasite taxonomic terms, which are used to mine for specific endoparasites. We found a large community of helminths and protozoans that were mostly restricted to the digestive tract and a few systemic parasites (e.g., Trypanosoma). Contrary to our expectations, all dendrobatid frogs regardless of the presence of alkaloid defenses have endoparasites, with their highest species richness located in the frog digestive tract. Some of these organisms (e.g., roundworms) might prove to be generalists, as they were not found to be co-diversifying with their frog hosts. We propose that endoparasites may escape poison frogs' chemical defenses by colonizing tissues with fewer alkaloids than the frog's skin

  9. Development of shuttle vectors for transformation of diverse Rickettsia species.

    Directory of Open Access Journals (Sweden)

    Nicole Y Burkhardt

    Full Text Available Plasmids have been identified in most species of Rickettsia examined, with some species maintaining multiple different plasmids. Three distinct plasmids were demonstrated in Rickettsia amblyommii AaR/SC by Southern analysis using plasmid specific probes. Copy numbers of pRAM18, pRAM23 and pRAM32 per chromosome in AaR/SC were estimated by real-time PCR to be 2.0, 1.9 and 1.3 respectively. Cloning and sequencing of R. amblyommii AaR/SC plasmids provided an opportunity to develop shuttle vectors for transformation of rickettsiae. A selection cassette encoding rifampin resistance and a fluorescent marker was inserted into pRAM18 yielding a 27.6 kbp recombinant plasmid, pRAM18/Rif/GFPuv. Electroporation of Rickettsia parkeri and Rickettsia bellii with pRAM18/Rif/GFPuv yielded GFPuv-expressing rickettsiae within 2 weeks. Smaller vectors, pRAM18dRG, pRAM18dRGA and pRAM32dRGA each bearing the same selection cassette, were made by moving the parA and dnaA-like genes from pRAM18 or pRAM32 into a vector backbone. R. bellii maintained the highest numbers of pRAM18dRGA (13.3 - 28.1 copies, and R. parkeri, Rickettsia monacensis and Rickettsia montanensis contained 9.9, 5.5 and 7.5 copies respectively. The same species transformed with pRAM32dRGA maintained 2.6, 2.5, 3.2 and 3.6 copies. pRM, the plasmid native to R. monacensis, was still present in shuttle vector transformed R. monacensis at a level similar to that found in wild type R. monacensis after 15 subcultures. Stable transformation of diverse rickettsiae was achieved with a shuttle vector system based on R. amblyommii plasmids pRAM18 and pRAM32, providing a new research tool that will greatly facilitate genetic and biological studies of rickettsiae.

  10. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    Science.gov (United States)

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  11. Studies on interaction of colloidal silver nanoparticles (SNPs) with five different bacterial species.

    Science.gov (United States)

    Khan, S Sudheer; Mukherjee, Amitava; Chandrasekaran, N

    2011-10-01

    Silver nanoparticles (SNPs) are being increasingly used in many consumer products like textile fabrics, cosmetics, washing machines, food and drug products owing to its excellent antimicrobial properties. Here we have studied the adsorption and toxicity of SNPs on bacterial species such as Pseudomonas aeruginosa, Micrococcus luteus, Bacillus subtilis, Bacillus barbaricus and Klebsiella pneumoniae. The influence of zeta potential on the adsorption of SNPs on bacterial cell surface was investigated at acidic, neutral and alkaline pH and with varying salt (NaCl) concentrations (0.05, 0.1, 0.5, 1 and 1.5 M). The survival rate of bacterial species decreased with increase in adsorption of SNPs. Maximum adsorption and toxicity was observed at pH 5, and NaCl concentration of 0.5 M, there by resulting in less toxicity. The zeta potential study suggests that, the adsorption of SNPs on the cell surface was related to electrostatic force of attraction. The equilibrium and kinetics of the adsorption process were also studied. The adsorption equilibrium isotherms fitted well to the Langmuir model. The kinetics of adsorption fitted best to pseudo-first-order. These findings form a basis for interpreting the interaction of nanoparticles with environmental bacterial species. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae

    Science.gov (United States)

    Grose, Julianne H.; Casjens, Sherwood R.

    2014-01-01

    Bacteriophages are the predominant biological entity on the planet. The recent explosion of sequence information has made estimates of their diversity possible. We describe the genomic comparison of 337 fully sequenced tailed phages isolated on 18 genera and 31 species of bacteria in the Enterobacteriaceae. These phages were largely unambiguously grouped into 56 diverse clusters (32 lytic and 24 temperate) that have syntenic similarity over >50% of the genomes within each cluster, but substantially less sequence similarity between clusters. Most clusters naturally break into sets of more closely related subclusters, 78% of which are correlated with their host genera. The largest groups of related phages are superclusters united by genome synteny to lambda (81 phages) and T7 (51 phages). This study forms a robust framework for understanding diversity and evolutionary relationships of existing tailed phages, for relating newly discovered phages and for determining host/phage relationships. PMID:25240328

  13. Decreased microbiota diversity associated with urinary tract infection in a trial of bacterial interference.

    Science.gov (United States)

    Horwitz, Deborah; McCue, Tyler; Mapes, Abigail C; Ajami, Nadim J; Petrosino, Joseph F; Ramig, Robert F; Trautner, Barbara W

    2015-09-01

    Patients with long-term indwelling catheters are at high risk of catheter-associated urinary tract infection (CAUTI). We hypothesized that colonizing the bladder with a benign Escherichia coli strain (E. coli HU2117, a derivative of E. coli 83972) would prevent CAUTI in older, catheterized adults. Adults with chronic, indwelling urinary catheters received study catheters that had been pre-coated with E. coli HU2117. We monitored the cultivatable organisms in the bladder for 28 days or until loss of E. coli HU2117. Urine from 4 subjects was collected longitudinally for 16S rRNA gene profiling. Eight of the ten subjects (average age 70.9 years) became colonized with E. coli HU2117, with a mean duration of 57.7 days (median: 28.5, range 0-266). All subjects also remained colonized by uropathogens. Five subjects suffered invasive UTI, 3 febrile UTI and 2 urosepsis/bacteremia, all associated with overgrowth of a urinary pathogen. Colonization with E. coli HU2117 did not impact bacterial bladder diversity, but subjects who developed infections had less diverse bladder microbiota. Colonization with E. coli HU2117 did not prevent bladder colonization or subsequent invasive disease by uropathogens. Microbial diversity may play a protective role against invasive infection of the catheterized bladder. ClinicalTrials.gov, NCT00554996 http://clinicaltrials.gov/ct2/show/NCT00554996. Published by Elsevier Ltd.

  14. Reducing Salt in Raw Pork Sausages Increases Spoilage and Correlates with Reduced Bacterial Diversity.

    Science.gov (United States)

    Fougy, Lysiane; Desmonts, Marie-Hélène; Coeuret, Gwendoline; Fassel, Christine; Hamon, Erwann; Hézard, Bernard; Champomier-Vergès, Marie-Christine; Chaillou, Stéphane

    2016-07-01

    Raw sausages are perishable foodstuffs; reducing their salt content raises questions about a possible increased spoilage of these products. In this study, we evaluated the influence of salt reduction (from 2.0% to 1.5% [wt/wt]), in combination with two types of packaging (modified atmosphere [50% mix of CO2-N2] and vacuum packaging), on the onset of spoilage and on the diversity of spoilage-associated bacteria. After 21 days of storage at 8°C, spoilage was easily observed, characterized by noticeable graying of the products and the production of gas and off-odors defined as rancid, sulfurous, or sour. At least one of these types of spoilage occurred in each sample, and the global spoilage intensity was more pronounced in samples stored under modified atmosphere than under vacuum packaging and in samples with the lower salt content. Metagenetic 16S rRNA pyrosequencing revealed that vacuum-packaged samples contained a higher total bacterial richness (n = 69 operational taxonomic units [OTUs]) than samples under the other packaging condition (n = 46 OTUs). The core community was composed of 6 OTUs (Lactobacillus sakei, Lactococcus piscium, Carnobacterium divergens, Carnobacterium maltaromaticum, Serratia proteamaculans, and Brochothrix thermosphacta), whereas 13 OTUs taxonomically assigned to the Enterobacteriaceae, Enterococcaceae, and Leuconostocaceae families comprised a less-abundant subpopulation. This subdominant community was significantly more abundant when 2.0% salt and vacuum packaging were used, and this correlated with a lower degree of spoilage. Our results demonstrate that salt reduction, particularly when it is combined with CO2-enriched packaging, promotes faster spoilage of raw sausages by lowering the overall bacterial diversity (both richness and evenness). Our study takes place in the context of raw meat product manufacturing and is linked to a requirement for salt reduction. Health guidelines are calling for a reduction in dietary salt intake

  15. Reducing Salt in Raw Pork Sausages Increases Spoilage and Correlates with Reduced Bacterial Diversity

    Science.gov (United States)

    Fougy, Lysiane; Desmonts, Marie-Hélène; Coeuret, Gwendoline; Fassel, Christine; Hamon, Erwann; Hézard, Bernard; Champomier-Vergès, Marie-Christine

    2016-01-01

    ABSTRACT Raw sausages are perishable foodstuffs; reducing their salt content raises questions about a possible increased spoilage of these products. In this study, we evaluated the influence of salt reduction (from 2.0% to 1.5% [wt/wt]), in combination with two types of packaging (modified atmosphere [50% mix of CO2-N2] and vacuum packaging), on the onset of spoilage and on the diversity of spoilage-associated bacteria. After 21 days of storage at 8°C, spoilage was easily observed, characterized by noticeable graying of the products and the production of gas and off-odors defined as rancid, sulfurous, or sour. At least one of these types of spoilage occurred in each sample, and the global spoilage intensity was more pronounced in samples stored under modified atmosphere than under vacuum packaging and in samples with the lower salt content. Metagenetic 16S rRNA pyrosequencing revealed that vacuum-packaged samples contained a higher total bacterial richness (n = 69 operational taxonomic units [OTUs]) than samples under the other packaging condition (n = 46 OTUs). The core community was composed of 6 OTUs (Lactobacillus sakei, Lactococcus piscium, Carnobacterium divergens, Carnobacterium maltaromaticum, Serratia proteamaculans, and Brochothrix thermosphacta), whereas 13 OTUs taxonomically assigned to the Enterobacteriaceae, Enterococcaceae, and Leuconostocaceae families comprised a less-abundant subpopulation. This subdominant community was significantly more abundant when 2.0% salt and vacuum packaging were used, and this correlated with a lower degree of spoilage. Our results demonstrate that salt reduction, particularly when it is combined with CO2-enriched packaging, promotes faster spoilage of raw sausages by lowering the overall bacterial diversity (both richness and evenness). IMPORTANCE Our study takes place in the context of raw meat product manufacturing and is linked to a requirement for salt reduction. Health guidelines are calling for a reduction in

  16. Pest species diversity enhances control of spider mites and whiteflies by a generalist phytoseiid predator

    NARCIS (Netherlands)

    Messelink, G.J.; Maanen, van R.; Holstein-Saj, van R.; Sabelis, M.W.; Janssen, A.

    2010-01-01

    To test the hypothesis that pest species diversity enhances biological pest control with generalist predators, we studied the dynamics of three major pest species on greenhouse cucumber: Western flower thrips, Frankliniella occidentalis (Pergande), greenhouse whitefly, Trialeurodes vaporariorum

  17. Species diversity and abundance of wild birds in Dagona-Waterfowl ...

    African Journals Online (AJOL)

    hope&shola

    The study of bird species diversity and richness in Dagona-Waterfowl sanctuary was carried out in early wet and late dry ... conservation of important species that rural inhabitants ... wetland of international importance on waterfowl habitat,.

  18. Novel Variants of Streptococcus thermophilus Bacteriophages Are Indicative of Genetic Recombination among Phages from Different Bacterial Species

    DEFF Research Database (Denmark)

    Szymczak, Paula; Janzen, Thomas; Neves, Ana Rute

    2017-01-01

    lactis P335 phages. Phage CHPC1151 was closely related to the atypical S. thermophilus phage 5093, homologous with a nondairy streptococcal prophage. By testing adsorption of the related streptococcal and lactococcal phages to the surface of S. thermophilus and L. lactis strains, we revealed....... thermophilus phages from the Chr. Hansen A/S collection, using PCR specific for the cos- or pac-type phages, as well as for the V2 antireceptor region. Three phages did not produce positive results with the assays. Analysis of phage morphologies indicated that two of these phages, CHPC577 and CHPC926, had...... the possibility of cross-interactions. Our data indicated that the use of S. thermophilus together with L. lactis, extensively applied for dairy fermentations, triggered the recombination between phages infecting different bacterial species. A notable diversity among S. thermophilus phage populations requires...

  19. Deep sequencing and ecological characterization of gut microbial communities of diverse bumble bee species.

    Directory of Open Access Journals (Sweden)

    Haw Chuan Lim

    Full Text Available Gut bacterial communities of bumble bees are correlated with defense against pathogens. Further understanding this host-microbe association is vitally important as bumble bees are currently experiencing global population declines, potentially due in part to emergent diseases. In this study, we used pyrosequencing and community fingerprinting (ARISA to characterize the gut microbial communities of nine bumble species from across the Bombus phylogeny. Overall, we delimited 74 bacterial taxa (operational taxonomic units or OTUs belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, Actinobacteria, Flavobacteria and Alphaproteobacteria. Each bacterial community was taxonomically simple, containing an average of 1.9 common (relative abundance per sample > 5% bacterial OTUs. The most abundant and prevalent (occurring in 92% of the samples bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi. Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment. The ARISA data showed a correlation between bacterial community structures and the geographic locations where the bees were sampled, suggesting that at least a subset of the bacterial species may be transmitted environmentally. Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera.

  20. Biochar amendment decreases soil microbial biomass and increases bacterial diversity in Moso bamboo (Phyllostachys edulis) plantations under simulated nitrogen deposition

    Science.gov (United States)

    Li, Quan; Lei, Zhaofeng; Song, Xinzhang; Zhang, Zhiting; Ying, Yeqing; Peng, Changhui

    2018-04-01

    Biochar amendment has been proposed as a strategy to improve acidic soils after overuse of nitrogen fertilizers. However, little is known of the role of biochar in soil microbial biomass carbon (MBC) and bacterial community structure and diversity after soil acidification induced by nitrogen (N) deposition. Using high-throughput sequencing of the 16S rRNA gene, we determined the effects of biochar amendment (BC0, 0 t bamboo biochar ha‑1 BC20, 20 t bamboo biochar ha‑1 and BC40, 40 t bamboo biochar ha‑1) on the soil bacterial community structure and diversity in Moso bamboo plantations that had received simulated N deposition (N30, 30 kg N ha‑1 yr‑1 N60, 60 kg N ha‑1 yr‑1 N90, 90 kg N ha‑1 yr‑1 and N-free) for 21 months. After treatment of N-free plots, BC20 significantly increased soil MBC and bacterial diversity, while BC40 significantly decreased soil MBC but increased bacterial diversity. When used to amend N30 and N60 plots, biochar significantly decreased soil MBC and the reducing effect increased with biochar amendment amount. However, these significant effects were not observed in N90 plots. Under N deposition, biochar amendment largely increased soil bacterial diversity, and these effects depended on the rates of N deposition and biochar amendment. Soil bacterial diversity was significantly related to the soil C/N ratio, pH, and soil organic carbon content. These findings suggest an optimal approach for using biochar to offset the effects of N deposition in plantation soils and provide a new perspective for understanding the potential role of biochar amendments in plantation soil.

  1. Patterns of Tree Species Diversity in Relation to Climatic Factors on the Sierra Madre Occidental, Mexico

    Science.gov (United States)

    Silva-Flores, Ramón; Pérez-Verdín, Gustavo; Wehenkel, Christian

    2014-01-01

    Biological diversity can be defined as variability among living organisms from all sources, including terrestrial organisms, marine and other aquatic ecosystems, and the ecological complexes which they are part of. This includes diversity within species, between species, and of ecosystems. Numerous diversity indices combine richness and evenness in a single expression, and several climate-based explanations have been proposed to explain broad-scale diversity patterns. However, climate-based water-energy dynamics appears to be an essential factor that determines patterns of diversity. The Mexican Sierra Madre Occidental occupies an area of about 29 million hectares and is located between the Neotropical and Holarctic ecozones. It shelters a high diversity of flora, including 24 different species of Pinus (ca. 22% on the whole), 54 species of Quercus (ca. 9–14%), 7 species of Arbutus (ca. 50%) and many other trees species. The objectives of this study were to model how tree species diversity is related to climatic and geographic factors and stand density and to test the Metabolic Theory, Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis, Mid-Domain Effect, and the Water-Energy Dynamic Theory on the Sierra Madre Occidental, Durango. The results supported the Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis and Water-Energy Dynamic Theory, but not the Mid-Domain Effect or Metabolic Theory. The annual aridity index was the variable most closely related to the diversity indices analyzed. Contemporary climate was found to have moderate to strong effects on the minimum, median and maximum tree species diversity. Because water-energy dynamics provided a satisfactory explanation for the patterns of minimum, median and maximum diversity, an understanding of this factor is critical to future biodiversity research. Quantile regression of the data showed that the three diversity parameters of tree species are generally higher in cold

  2. Patterns of tree species diversity in relation to climatic factors on the Sierra Madre Occidental, Mexico.

    Science.gov (United States)

    Silva-Flores, Ramón; Pérez-Verdín, Gustavo; Wehenkel, Christian

    2014-01-01

    Biological diversity can be defined as variability among living organisms from all sources, including terrestrial organisms, marine and other aquatic ecosystems, and the ecological complexes which they are part of. This includes diversity within species, between species, and of ecosystems. Numerous diversity indices combine richness and evenness in a single expression, and several climate-based explanations have been proposed to explain broad-scale diversity patterns. However, climate-based water-energy dynamics appears to be an essential factor that determines patterns of diversity. The Mexican Sierra Madre Occidental occupies an area of about 29 million hectares and is located between the Neotropical and Holarctic ecozones. It shelters a high diversity of flora, including 24 different species of Pinus (ca. 22% on the whole), 54 species of Quercus (ca. 9-14%), 7 species of Arbutus (ca. 50%) and many other trees species. The objectives of this study were to model how tree species diversity is related to climatic and geographic factors and stand density and to test the Metabolic Theory, Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis, Mid-Domain Effect, and the Water-Energy Dynamic Theory on the Sierra Madre Occidental, Durango. The results supported the Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis and Water-Energy Dynamic Theory, but not the Mid-Domain Effect or Metabolic Theory. The annual aridity index was the variable most closely related to the diversity indices analyzed. Contemporary climate was found to have moderate to strong effects on the minimum, median and maximum tree species diversity. Because water-energy dynamics provided a satisfactory explanation for the patterns of minimum, median and maximum diversity, an understanding of this factor is critical to future biodiversity research. Quantile regression of the data showed that the three diversity parameters of tree species are generally higher in cold

  3. Impact of commonly used agrochemicals on bacterial diversity in cultivated soils.

    Science.gov (United States)

    Ampofo, J A; Tetteh, W; Bello, M

    2009-09-01

    The effects of three selected agrochemicals on bacterial diversity in cultivated soil have been studied. The selected agrochemicals are Cerox (an insecticide), Ceresate and Paraquat (both herbicides). The effect on bacterial population was studied by looking at the total heterotrophic bacteria presence and the effect of the agrochemicals on some selected soil microbes. The soil type used was loamy with pH of 6.0-7.0. The soil was placed in opaque pots and bambara bean (Vigna subterranean) seeds cultivated in them. The agrochemicals were applied two weeks after germination of seeds at concentrations based on manufacturer's recommendation. Plant growth was assessed by weekly measurement of plant height, foliage appearance and number of nodules formed after one month. The results indicated that the diversity index (Di) among the bacteria populations in untreated soil and that of Cerox-treated soils were high with mean diversity index above 0.95. Mean Di for Ceresate-treated soil was 0.88, and that for Paraquattreated soil was 0.85 indicating low bacterial populations in these treatment-type soils. The study also showed that application of the agrochemicals caused reduction in the number of total heterotrophic bacteria population sizes in the soil. Ceresate caused 82.50% reduction in bacteria number from a mean of 40 × 10(5) cfu g(-1) of soil sample to 70 × 10(4) cfu g(-1). Paraquat-treated soil showed 92.86% reduction, from a mean of 56 × 10(5) cfu g(-1) to 40 × 10(4) cfu g(-1). Application of Cerox to the soil did not have any remarkable reduction in bacterial population number. Total viable cell count studies using Congo red yeast-extract mannitol agar indicated reduction in the number of Rhizobium spp. after application of the agrochemicals. Mean number of Rhizobium population numbers per gram of soil was 180 × 10(4) for the untreated soil. Cerox-treated soil recorded mean number of 138 × 10(4) rhizobial cfu g(-1) of soil, a 23.33% reduction. Ceresate- and

  4. Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

    Science.gov (United States)

    Lowrey, Liam; Woodhams, Douglas C.; Tacchi, Luca

    2015-01-01

    The mucosal surfaces of wild and farmed aquatic vertebrates face the threat of many aquatic pathogens, including fungi. These surfaces are colonized by diverse symbiotic bacterial communities that may contribute to fight infection. Whereas the gut microbiome of teleosts has been extensively studied using pyrosequencing, this tool has rarely been employed to study the compositions of the bacterial communities present on other teleost mucosal surfaces. Here we provide a topographical map of the mucosal microbiome of an aquatic vertebrate, the rainbow trout (Oncorhynchus mykiss). Using 16S rRNA pyrosequencing, we revealed novel bacterial diversity at each of the five body sites sampled and showed that body site is a strong predictor of community composition. The skin exhibited the highest diversity, followed by the olfactory organ, gills, and gut. Flectobacillus was highly represented within skin and gill communities. Principal coordinate analysis and plots revealed clustering of external sites apart from internal sites. A highly diverse community was present within the epithelium, as demonstrated by confocal microscopy and pyrosequencing. Using in vitro assays, we demonstrated that two Arthrobacter sp. skin isolates, a Psychrobacter sp. strain, and a combined skin aerobic bacterial sample inhibit the growth of Saprolegnia australis and Mucor hiemalis, two important aquatic fungal pathogens. These results underscore the importance of symbiotic bacterial communities of fish and their potential role for the control of aquatic fungal diseases. PMID:26209676

  5. Bacterial strains diversity in Musa spp. phyllosphere with antifungal activity against Mycosphaerella fijiensis Morelet

    Directory of Open Access Journals (Sweden)

    Mileidy Cruz-Martín

    2016-01-01

    Full Text Available The search for alternatives to agricultural pesticides used for the management of black Sigatoka (Mycosphaerella fijiensis Morelet includes the selection of microorganisms strains with potential for the control of this pathogen. The objective of the work was to characterize bacterial strains isolated from the phylosphere of Musa spp. with antifungal effect against M. fijiensis. A morphological, cultural, physiological and molecular characterization of the strains was performed and the antifungal activity of these strains was quantified by dual culture. It was verified the diversity of bacteria with antifungal properties against M. fijiensis present in the phylosphere of Musa spp.  In addition, it was found that the phyllosphere of these crops can be used as a source of obtaining possible biological controls of M. fijiensis.   Keywords: bacteria, biocontrol, Black Sigatoka, epiphytes

  6. Molecular analysis of the bacterial diversity in a specialized consortium for diesel oil degradation

    Energy Technology Data Exchange (ETDEWEB)

    Paixao, Douglas Antonio Alvaredo; Accorsini, Fabio Raphael; Vidotti, Maria Benincasa; Lemos, Eliana Gertrudes de Macedo [Universidade Estadual Paulista (FCAV/UNESP), Jaboticabal, SP (Brazil). Fac. de Ciencias Agrarias e Veterinarias], Emails: douglas_unespfcav@yahoo.com.br, vidotti@netsite.com.bregerle@fcav.unesp.br; Dimitrov, Mauricio Rocha [Universidade de Sao Paulo (USP), SP (Brazil)], Email: mau_dimitrov@yahoo.com.br; Pereira, Rodrigo Matheus [EMBRAPARA Soybean - Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA - Soja), Londrina, PR (Brazil)], Email: poetbr@gmail.com

    2010-05-15

    Diesel oil is a compound derived from petroleum, consisting primarily of hydrocarbons. Poor conditions in transportation and storage of this product can contribute significantly to accidental spills causing serious ecological problems in soil and water and affecting the diversity of the microbial environment. The cloning and sequencing of the 16S rRNA gene is one of the molecular techniques that allows estimation and comparison of the microbial diversity in different environmental samples. The aim of this work was to estimate the diversity of microorganisms from the Bacteria domain in a consortium specialized in diesel oil degradation through partial sequencing of the 16S rRNA gene. After the extraction of DNA metagenomics, the material was amplified by PCR reaction using specific oligonucleotide primers for the 16S rRNA gene. The PCR products were cloned into a pGEM-T-Easy vector (Promega), and Escherichia coli was used as the host cell for recombinant DNAs. The partial clone sequencing was obtained using universal oligonucleotide primers from the vector. The genetic library obtained generated 431 clones. All the sequenced clones presented similarity to phylum Proteobacteria, with Gammaproteobacteria the most present group (49.8 % of the clones), followed by Alphaproteobacteira (44.8 %) and Betaproteobacteria (5.4 %). The Pseudomonas genus was the most abundant in the metagenomics library, followed by the Parvibaculum and the Sphingobium genus, respectively. After partial sequencing of the 16S rRNA, the diversity of the bacterial consortium was estimated using DOTUR software. When comparing these sequences to the database from the National Center for Biotechnology Information (NCBI), a strong correlation was found between the data generated by the software used and the data deposited in NCBI. (author)

  7. Limited Bacterial Diversity within a Treatment Plant Receiving Antibiotic-Containing Waste from Bulk Drug Production

    Science.gov (United States)

    Shouche, Yogesh S.; Larsson, D. G. Joakim

    2016-01-01

    Biological treatment of waste water from bulk drug production, contaminated with high levels of fluoroquinolone antibiotics, can lead to massive enrichment of antibiotic resistant bacteria, resistance genes and associated mobile elements, as previously shown. Such strong selection may be boosted by the use of activated sludge (AS) technology, where microbes that are able to thrive on the chemicals within the wastewater are reintroduced at an earlier stage of the process to further enhance degradation of incoming chemicals. The microbial community structure within such a treatment plant is, however, largely unclear. In this study, Illumina-based 16S rRNA amplicon sequencing was applied to investigate the bacterial communities of different stages from an Indian treatment plant operated by Patancheru Environment Technology Limited (PETL) in Hyderabad, India. The plant receives waste water with high levels of fluoroquinolones and applies AS technology. A total of 1,019,400 sequences from samples of different stages of the treatment process were analyzed. In total 202, 303, 732, 652, 947 and 864 operational taxonomic units (OTUs) were obtained at 3% distance cutoff in the equilibrator, aeration tanks 1 and 2, settling tank, secondary sludge and old sludge samples from PETL, respectively. Proteobacteria was the most dominant phyla in all samples with Gammaproteobacteria and Betaproteobacteria being the dominant classes. Alcaligenaceae and Pseudomonadaceae, bacterial families from PETL previously reported to be highly multidrug resistant, were the dominant families in aeration tank samples. Despite regular addition of human sewage (approximately 20%) to uphold microbial activity, the bacterial diversity within aeration tanks from PETL was considerably lower than corresponding samples from seven, regular municipal waste water treatment plants. The strong selection pressure from antibiotics present may be one important factor in structuring the microbial community in PETL

  8. Limited Bacterial Diversity within a Treatment Plant Receiving Antibiotic-Containing Waste from Bulk Drug Production.

    Science.gov (United States)

    Marathe, Nachiket P; Shetty, Sudarshan A; Shouche, Yogesh S; Larsson, D G Joakim

    2016-01-01

    Biological treatment of waste water from bulk drug production, contaminated with high levels of fluoroquinolone antibiotics, can lead to massive enrichment of antibiotic resistant bacteria, resistance genes and associated mobile elements, as previously shown. Such strong selection may be boosted by the use of activated sludge (AS) technology, where microbes that are able to thrive on the chemicals within the wastewater are reintroduced at an earlier stage of the process to further enhance degradation of incoming chemicals. The microbial community structure within such a treatment plant is, however, largely unclear. In this study, Illumina-based 16S rRNA amplicon sequencing was applied to investigate the bacterial communities of different stages from an Indian treatment plant operated by Patancheru Environment Technology Limited (PETL) in Hyderabad, India. The plant receives waste water with high levels of fluoroquinolones and applies AS technology. A total of 1,019,400 sequences from samples of different stages of the treatment process were analyzed. In total 202, 303, 732, 652, 947 and 864 operational taxonomic units (OTUs) were obtained at 3% distance cutoff in the equilibrator, aeration tanks 1 and 2, settling tank, secondary sludge and old sludge samples from PETL, respectively. Proteobacteria was the most dominant phyla in all samples with Gammaproteobacteria and Betaproteobacteria being the dominant classes. Alcaligenaceae and Pseudomonadaceae, bacterial families from PETL previously reported to be highly multidrug resistant, were the dominant families in aeration tank samples. Despite regular addition of human sewage (approximately 20%) to uphold microbial activity, the bacterial diversity within aeration tanks from PETL was considerably lower than corresponding samples from seven, regular municipal waste water treatment plants. The strong selection pressure from antibiotics present may be one important factor in structuring the microbial community in PETL

  9. Limited Bacterial Diversity within a Treatment Plant Receiving Antibiotic-Containing Waste from Bulk Drug Production.

    Directory of Open Access Journals (Sweden)

    Nachiket P Marathe

    Full Text Available Biological treatment of waste water from bulk drug production, contaminated with high levels of fluoroquinolone antibiotics, can lead to massive enrichment of antibiotic resistant bacteria, resistance genes and associated mobile elements, as previously shown. Such strong selection may be boosted by the use of activated sludge (AS technology, where microbes that are able to thrive on the chemicals within the wastewater are reintroduced at an earlier stage of the process to further enhance degradation of incoming chemicals. The microbial community structure within such a treatment plant is, however, largely unclear. In this study, Illumina-based 16S rRNA amplicon sequencing was applied to investigate the bacterial communities of different stages from an Indian treatment plant operated by Patancheru Environment Technology Limited (PETL in Hyderabad, India. The plant receives waste water with high levels of fluoroquinolones and applies AS technology. A total of 1,019,400 sequences from samples of different stages of the treatment process were analyzed. In total 202, 303, 732, 652, 947 and 864 operational taxonomic units (OTUs were obtained at 3% distance cutoff in the equilibrator, aeration tanks 1 and 2, settling tank, secondary sludge and old sludge samples from PETL, respectively. Proteobacteria was the most dominant phyla in all samples with Gammaproteobacteria and Betaproteobacteria being the dominant classes. Alcaligenaceae and Pseudomonadaceae, bacterial families from PETL previously reported to be highly multidrug resistant, were the dominant families in aeration tank samples. Despite regular addition of human sewage (approximately 20% to uphold microbial activity, the bacterial diversity within aeration tanks from PETL was considerably lower than corresponding samples from seven, regular municipal waste water treatment plants. The strong selection pressure from antibiotics present may be one important factor in structuring the microbial

  10. Novel Bacterial Proteins and Lipids Reveal the Diversity of Triterpenoid Biomarker Synthesis

    Science.gov (United States)

    Wei, J. H.; Banta, A. B.; Gill, C. C. C.; Giner, J. L.; Welander, P. V.

    2017-12-01

    Lipids preserved in sediments and rocks function as organic biomarkers providing evidence for the types of organisms that lived in ancient environments. We use a combined approach utilizing comparative genomics, molecular biology, and lipid analysis to discover novel cyclic triteprenoid lipids and their biosynthetic pathways in bacteria. Here, we present two cases of bacterial synthesis of pentacylic triterpenols previously thought to be indicative of eukaryotes, which address current incongruities in the fossil record. Cyclic triterpenoid lipids, such as hopanoids and sterols, are generally associated with bacteria and eukaryotes, respectively. The pentacyclic triterpenoid tetrahymanol, first discovered in the ciliate Tetrahymena pyriformis, and its diagenetic product gammacerane, have been previously interpreted as markers for eukaryotes and linked to water column stratification. Yet the occurrence of tetrahymanol in bacteria implies our knowledge of extant tetrahymanol producers is not complete. Through comparative genomics we identified a new gene required for tetrahymanol synthesis in the bacterium Methylomicrobium alcaliphilum. This gene encodes a novel enzyme, Tetrahymanol synthase (THS), that synthesizes tetrahymanol from the hopanoid diploptene demonstrating a pathway for tetrahymanol production in bacteria distinct from that in eukaryotes. We bionformatically identified THS homologs in 104 bacterial genomes and 472 metagenomes, implying a great diversity of tetrahymanol producers. Lipids of the arborane class, such as iso-arborinol, are commonly found in modern angiosperms. Arobranes are synthesized by the enzyme oxidosqualene cyclase (OSC), which in plants can form both tetra and pentacyclic molecules. While bacteria are known to produce tetracyclic sterol compounds, bacterial synthesis of pentacyclic arborane class triterpenols of this class were previously undiscovered. We have identified a bacterium, Eudoraea adriatica, whose OSC synthesizes

  11. Bacterial diversity and composition of an alkaline uranium mine tailings-water interface.

    Science.gov (United States)

    Khan, Nurul H; Bondici, Viorica F; Medihala, Prabhakara G; Lawrence, John R; Wolfaardt, Gideon M; Warner, Jeff; Korber, Darren R

    2013-10-01

    The microbial diversity and biogeochemical potential associated with a northern Saskatchewan uranium mine water-tailings interface was examined using culture-dependent and -independent techniques. Morphologically-distinct colonies from uranium mine water-tailings and a reference lake (MC) obtained using selective and non-selective media were selected for 16S rRNA gene sequencing and identification, revealing that culturable organisms from the uranium tailings interface were dominated by Firmicutes and Betaproteobacteria; whereas, MC organisms mainly consisted of Bacteroidetes and Gammaproteobacteria. Ion Torrent (IT) 16S rRNA metagenomic analysis carried out on extracted DNA from tailings and MC interfaces demonstrated the dominance of Firmicutes in both of the systems. Overall, the tailings-water interface environment harbored a distinct bacterial community relative to the MC, reflective of the ambient conditions (i.e., total dissolved solids, pH, salinity, conductivity, heavy metals) dominating the uranium tailings system. Significant correlations among the physicochemical data and the major bacterial groups present in the tailings and MC were also observed. Presence of sulfate reducing bacteria demonstrated by culture-dependent analyses and the dominance of Desulfosporosinus spp. indicated by Ion Torrent analyses within the tailings-water interface suggests the existence of anaerobic microenvironments along with the potential for reductive metabolic processes.

  12. Measuring species diversity in a subtropical forest across a tree size gradient: a comparison of diversity indices

    International Nuclear Information System (INIS)

    Ke, X.; Su, Z.; Hu, Y.; Zhou, Y.; Xu, M.

    2017-01-01

    Shannon-Wiener index and Simpson's diversity index together with other metrics, e.g., richness, number of stems per species or species-specific density (N: S ratio), and kurtosis, were applied to characterize the woody plant diversity patterns of a subtropical broadleaved forest in south China. The aims of our study were to compare the efficacy and sensitivity to community diversity measures between Shannon-Wiener index and Simpson's diversity index. Tree census data from a 5-ha sample plot was partitioned into 3 datasets by diameter class to represent 3 distinct woody plant communities for the characterization of diversity across communities. The 5-ha sample plot of the forest had a total abundance of 23,301 tree stems = 1 cm DBH and a richness of 139 species. The majority of tree stems were seedlings (41.1%) and saplings (38.8%), whereas canopy trees only accounted for 20.1% of the total tree stems. Both Shannon-Wiener index and Simpson's diversity index decreased significantly in response to a decrease in the N: S ratio across the datasets, but Shannon-Wiener index was more sensitive to plot-based richness changes and had a higher efficacy in predicting changes in species richness. Our findings are contrary to the general belief that Shannon-Wiener index is an insensitive measure of the character of the N: S relationship and have demonstrated that it remains a good measure for species diversity in plant community studies for its sensitivity and efficacy. We also suggest that the kurtosis statistic can be used as a new diversity measure due to its sensitivity to diversity change. (author)

  13. Plant-associated bacterial populations on native and invasive plant species: comparisons between 2 freshwater environments.

    Science.gov (United States)

    Olapade, Ola A; Pung, Kayleigh

    2012-06-01

    Plant-microbial interactions have been well studied because of the ecological importance of such relationships in aquatic systems. However, general knowledge regarding the composition of these biofilm communities is still evolving, partly as a result of several confounding factors that are attributable to plant host properties and to hydrodynamic conditions in aquatic environments. In this study, the occurrences of various bacterial phylogenetic taxa on 2 native plants, i.e., mayapple (Podophyllum peltatum L.) and cow parsnip (Heracleum maximum Bartram), and on an invasive species, i.e., garlic mustard (Alliaria petiolata (M. Bieb.) Cavara & Grande), were quantitatively examined using nucleic acid staining and fluorescence in situ hybridization. The plants were incubated in triplicates for about a week within the Kalamazoo River and Pierce Cedar Creek as well as in microcosms. The bacterial groups targeted for enumeration are known to globally occur in relatively high abundance and are also ubiquitously distributed in freshwater environments. Fluorescence in situ hybridization analyses of the bacterioplankton assemblages revealed that the majority of bacterial cells that hybridized with the different probes were similar between the 2 sites. In contrast, the plant-associated populations while similar on the 3 plants incubated in Kalamazoo River, their representations were highest on the 2 native plants relative to the invasive species in Pierce Cedar Creek. Overall, our results further suggested that epiphytic bacterial assemblages are probably under the influences of and probably subsequently respond to multiple variables and conditions in aquatic milieus.

  14. Combinations of bacterial species associated with symptomatic endodontic infections in a Chinese population.

    Science.gov (United States)

    Qi, Z; Cao, H; Jiang, H; Zhao, J; Tang, Z

    2016-01-01

    To use microarrays to detect 11 selected bacteria in infected root canals, revealing bacterial combinations that are associated with clinical symptoms and signs of primary endodontic infections in a Chinese population. DNA was extracted from 90 samples collected from the root canals of teeth with primary endodontic infections in a Chinese population, and the 16S rRNA gene was amplified by polymerase chain reaction (PCR). The PCR products were hybridized to microarrays containing specific oligonucleotide probes targeting 11 species, and the arrays were screened with a confocal laser scanner. Pearson's chi-squared test and cluster analysis were performed to investigate the associations between the bacterial combinations and clinical symptoms and signs using SAS 8.02. Seventy-seven samples (86%) yielded at least one of the 11 target species. Parvimonas micra (56%), Porphyromonas endodontalis (51%), Tannerella forsythia (48%), Prevotella intermedia (44%) and Porphyromonas gingivalis (37%) were the most prevalent taxa and were often concomitant. The following positive associations were found between the bacterial combinations and clinical features: P. endodontalis and T. forsythia with abscess; P. gingivalis and P. micra with sinus tract; P. gingivalis and P. endodontalis or P. micra and P. endodontalis with abscess and sinus tract; and the combination of P. endodontalis, P. micra, T. forsythia and P. gingivalis with sinus tract (P endodontalis, T. forsythia and P. gingivalis may contribute to abscesses or sinus tracts of endodontic origin with bacterial synergism in a Chinese population. © 2015 International Endodontic Journal. Published by John Wiley & Sons Ltd.

  15. Individuals and the variation needed for high species diversity in forest trees

    Science.gov (United States)

    James S. Clark

    2010-01-01

    In the past, explanations for high species diversity have been sought at the species level. Theory shows that coexistence requires substantial differences between species, but species-level data rarely provide evidence for such differences. Using data from forests in the southeastern United States, I show here that variation evident at the individual level provides for...

  16. Bacterial community dynamics in a cooling tower with emphasis on pathogenic bacteria and Legionella species using universal and genus-specific deep sequencing.

    Science.gov (United States)

    Pereira, Rui P A; Peplies, Jörg; Höfle, Manfred G; Brettar, Ingrid

    2017-10-01

    Cooling towers are the major source of outbreaks of legionellosis in Europe and worldwide. These outbreaks are mostly associated with Legionella species, primarily L. pneumophila, and its surveillance in cooling tower environments is of high relevance to public health. In this study, a combined NGS-based approach was used to study the whole bacterial community, specific waterborne and water-based bacterial pathogens, especially Legionella species, targeting the 16S rRNA gene. This approach was applied to water from a cooling tower obtained by monthly sampling during two years. The studied cooling tower was an open circuit cooling tower with lamellar cooling situated in Braunschweig, Germany. A highly diverse bacterial community was observed with 808 genera including 25 potentially pathogenic taxa using universal 16S rRNA primers. Sphingomonas and Legionella were the most abundant pathogenic genera. By applying genus-specific primers for Legionella, a diverse community with 85 phylotypes, and a representative core community with substantial temporal heterogeneity was observed. A high percentage of sequences (65%) could not be affiliated to an acknowledged species. L. pneumophila was part of the core community and the most abundant Legionella species reinforcing the importance of cooling towers as its environmental reservoir. Major temperature shifts (>10 °C) were the key environmental factor triggering the reduction or dominance of the Legionella species in the Legionella community dynamics. In addition, interventions by chlorine dioxide had a strong impact on the Legionella community composition but not on the whole bacterial community. Overall, the presented results demonstrated the value of a combined NGS approach for the molecular monitoring and surveillance of health related pathogens in man-made freshwater systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Bacterial communities of disease vectors sampled across time, space, and species.

    Science.gov (United States)

    Jones, Ryan T; Knight, Rob; Martin, Andrew P

    2010-02-01

    A common strategy of pathogenic bacteria is to form close associations with parasitic insects that feed on animals and to use these insects as vectors for their own transmission. Pathogens interact closely with other coexisting bacteria within the insect, and interactions between co-occurring bacteria may influence the vector competency of the parasite. Interactions between particular lineages can be explored through measures of alpha-diversity. Furthermore, general patterns of bacterial community assembly can be explored through measures of beta-diversity. Here, we use pyrosequencing (n=115,924 16S rRNA gene sequences) to describe the bacterial communities of 230 prairie dog fleas sampled across space and time. We use these communinty characterizations to assess interactions between dominant community members and to explore general patterns of bacterial community assembly in fleas. An analysis of co-occurrence patterns suggests non-neutral negative interactions between dominant community members (Pspace (phylotype-based: R=0.418, Pspace and time.

  18. Chemically emulsified crude oil as substrate for bacterial oxidation : differences in species response

    International Nuclear Information System (INIS)

    Bruheim, P.; Eimhjellen, K.

    1998-01-01

    The ability of bacterial species to oxidize alkanes in crude oil in water emulsions was studied. Alkanes in crude oil need specific physiological adaptations to the microorganisms. Synthesis of biosurfactants has been considered as a prerequisite for either specific adhesion mechanisms to large oil drops or emulsification of oil followed by uptake of submicron oil droplets. In this study four bacterial species were tested. Emulsions were prepared by nonionic sorbitan ester and polyoxyethylene ether surfactants. The oxidation rates were measured. Both positive and negative effects of surfactant amendments were observed. The same surfactant affected different bacteria in different ways. The response to the surfactant amendment depended on the physiological state of the bacteria. The results showed that surfactants resulted in decreased cell adhesion to the oil phase for all the bacteria. 19 refs., 3 tabs., 4 figs

  19. Consumer preference for seeds and seedlings of rare species impacts tree diversity at multiple scales.

    Science.gov (United States)

    Young, Hillary S; McCauley, Douglas J; Guevara, Roger; Dirzo, Rodolfo

    2013-07-01

    Positive density-dependent seed and seedling predation, where herbivores selectively eat seeds or seedlings of common species, is thought to play a major role in creating and maintaining plant community diversity. However, many herbivores and seed predators are known to exhibit preferences for rare foods, which could lead to negative density-dependent predation. In this study, we first demonstrate the occurrence of increased predation of locally rare tree species by a widespread group of insular seed and seedling predators, land crabs. We then build computer simulations based on these empirical data to examine the effects of such predation on diversity patterns. Simulations show that herbivore preferences for locally rare species are likely to drive scale-dependent effects on plant community diversity: at small scales these foraging patterns decrease plant community diversity via the selective consumption of rare plant species, while at the landscape level they should increase diversity, at least for short periods, by promoting clustered local dominance of a variety of species. Finally, we compared observed patterns of plant diversity at the site to those obtained via computer simulations, and found that diversity patterns generated under simulations were highly consistent with observed diversity patterns. We posit that preference for rare species by herbivores may be prevalent in low- or moderate-diversity systems, and that these effects may help explain diversity patterns across different spatial scales in such ecosystems.

  20. Expanding diversity of potential bacterial partners of the methanotrophic ANME archaea using Magneto-FISH

    Science.gov (United States)

    Trembath-Reichert, E.; Green-Saxena, A.; Steele, J. A.; Orphan, V. J.

    2012-12-01

    Sulfate-coupled anaerobic oxidation of methane (AOM) in marine sediments is the major sink for methane in the oceans. This process is believed to be catalyzed by as yet uncultured syntrophic consortia of ANME archaea (affiliated with the Methanosarcinales) and sulfate-reducing bacteria belonging to the Desulfosarcina/Desulfococcus and Desulfobulbaceae. These syntrophic consortia have been described from methane-rich habitats worldwide and appear to be most concentrated in areas of high methane flux, such as cold seeps along continental margins. The extent of the diversity and ecophysiological potential of these microbial associations is still poorly constrained. In an effort to better characterize the diversity of microorganisms forming associations with different clades of methanotrophic ANME archaea (ANME-1, ANME-2a/b/c, ANME-3) and link these organisms to potentially diagnostic metabolic genes (e.g. mcrA, dsrAB, aprA), we employed a unique culture-independent whole cell capture technique which combines Fluorescence In Situ Hybridization with immuno-magnetic cell capture (Magneto-FISH). We used Magneto-FISH for targeted enrichment of specific ANME groups and their associated bacteria directly from formalin- and ethanol-fixed methane seep sediment. The identity and metabolic gene diversity of captured microorganisms were then assessed by clone library construction and sequencing. Diversity recovered from Magneto-FISH experiments using general and clade-specific ANME targeted probes show both the expected selectivity of the FISH probes (i.e. predominately ANME-2c subclade captured with an ANME-2c probe and multiple ANME groups recovered with the general probe targeting most ANME). Follow up FISH experiments were conducted to confirm physical associations between ANME and unique bacterial members (deltaproteobacteria and other non-sulfate reducing groups) that were common to multiple Magneto-FISH capture experiments. Analyses of metabolic gene diversity for archaeal

  1. Effects of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil

    DEFF Research Database (Denmark)

    Rasmussen, Lasse Dam; Sørensen, S. J.

    2001-01-01

    This study investigates the effect of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil. The changes in diversity were monitored in soil microcosms, enriched with 25 mug Hg(II) g(-1) soil, over a period of 3 months...... by purification of total soil DNA and amplification of bacterial 16S rDNA fragments by polymerase chain reaction. Concentrations of bioavailable and total mercury were measured throughout the experiment. The effect on the culturable heterotrophic and genetic diversity was very similar, showing an immediate...... decrease after mercury addition but then slowly increasing throughout the entire experimental period. Pre-exposure levels were not reached within the time span of this investigation. The DGGE band pattern indicated that a shift in the community structure was responsible for recovered diversity. When...

  2. Surface-Selective Preferential Production of Reactive Oxygen Species on Piezoelectric Ceramics for Bacterial Killing

    OpenAIRE

    Tan, Guoxin; Wang, Shuangying; Zhu, Ye; Zhou, Lei; Yu, Peng; Wang, Xiaolan; He, Tianrui; Chen, Junqi; Mao, Chuanbin; Ning, Chengyun

    2016-01-01

    Reactive oxygen species (ROS) can be used to kill bacterial cells, and thus the selective generation of ROS from material surfaces is an emerging direction in antibacterial material discovery. We found the polarization of piezoelectric ceramic causes the two sides of the disk to become positively and negatively charged, which translate into cathode and anode surfaces in an aqueous solution. Because of the microelectrolysis of water, ROS are preferentially formed on the cathode surface. Conseq...

  3. Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.: Implication for Conservation and Agricultural Practices.

    Directory of Open Access Journals (Sweden)

    Marie Florence Sandrine Ngo Ngwe

    Full Text Available Yams (Dioscorea spp. consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.

  4. Expanding the species and chemical diversity of Penicillium section Cinnamopurpurea

    DEFF Research Database (Denmark)

    Peterson, Stephen W.; Jurjević, Željko; Frisvad, Jens Christian

    2015-01-01

    isolates and sequenced. Two species in section Cinnamopurpurea are self-compatible sexual species, but the asexual species had polymorphic loci suggestive of sexual reproduction and variation in conidium size suggestive of ploidy level differences typical of heterothallism. Accordingly we use genealogical...... concordance analysis, a technique valid only in heterothallic organisms, for putatively asexual species. Seven new species were revealed in the analysis and are described here. Extrolite analysis showed that two of the new species, P. colei and P. monsserratidens produce the mycotoxin citreoviridin that has...

  5. High phylogenetic diversity is preserved in species-poor high-elevation temperate moth assemblages

    NARCIS (Netherlands)

    Zou, Yi; Sang, Weiguo; Hausmann, Axel; Axmacher, Jan Christoph

    2016-01-01

    Understanding the diversity and composition of species assemblages and identifying underlying biotic and abiotic determinants represent great ecological challenges. Addressing some of these issues, we investigated the α-diversity and phylogenetic composition of species-rich geometrid moth

  6. Soil phosphorus heterogeneity promotes tree species diversity and phylogenetic clustering in a tropical seasonal rainforest.

    Science.gov (United States)

    Xu, Wumei; Ci, Xiuqin; Song, Caiyun; He, Tianhua; Zhang, Wenfu; Li, Qiaoming; Li, Jie

    2016-12-01

    The niche theory predicts that environmental heterogeneity and species diversity are positively correlated in tropical forests, whereas the neutral theory suggests that stochastic processes are more important in determining species diversity. This study sought to investigate the effects of soil nutrient (nitrogen and phosphorus) heterogeneity on tree species diversity in the Xishuangbanna tropical seasonal rainforest in southwestern China. Thirty-nine plots of 400 m 2 (20 × 20 m) were randomly located in the Xishuangbanna tropical seasonal rainforest. Within each plot, soil nutrient (nitrogen and phosphorus) availability and heterogeneity, tree species diversity, and community phylogenetic structure were measured. Soil phosphorus heterogeneity and tree species diversity in each plot were positively correlated, while phosphorus availability and tree species diversity were not. The trees in plots with low soil phosphorus heterogeneity were phylogenetically overdispersed, while the phylogenetic structure of trees within the plots became clustered as heterogeneity increased. Neither nitrogen availability nor its heterogeneity was correlated to tree species diversity or the phylogenetic structure of trees within the plots. The interspecific competition in the forest plots with low soil phosphorus heterogeneity could lead to an overdispersed community. However, as heterogeneity increase, more closely related species may be able to coexist together and lead to a clustered community. Our results indicate that soil phosphorus heterogeneity significantly affects tree diversity in the Xishuangbanna tropical seasonal rainforest, suggesting that deterministic processes are dominant in this tropical forest assembly.

  7. Links between plant litter chemistry, species diversity, and below-ground ecosystem function.

    Science.gov (United States)

    Meier, Courtney L; Bowman, William D

    2008-12-16

    Decomposition is a critical source of plant nutrients, and drives the largest flux of terrestrial C to the atmosphere. Decomposing soil organic matter typically contains litter from multiple plant species, yet we lack a mechanistic understanding of how species diversity influences decomposition processes. Here, we show that soil C and N cycling during decomposition are controlled by the composition and diversity of chemical compounds within plant litter mixtures, rather than by simple metrics of plant species diversity. We amended native soils with litter mixtures containing up to 4 alpine plant species, and we used 9 litter chemical traits to evaluate the chemical composition (i.e., the identity and quantity of compounds) and chemical diversity of the litter mixtures. The chemical composition of the litter mixtures was the strongest predictor of soil respiration, net N mineralization, and microbial biomass N. Soil respiration and net N mineralization rates were also significantly correlated with the chemical diversity of the litter mixtures. In contrast, soil C and N cycling rates were poorly correlated with plant species richness, and there was no relationship between species richness and the chemical diversity of the litter mixtures. These results indicate that the composition and diversity of chemical compounds in litter are potentially important functional traits affecting decomposition, and simple metrics like plant species richness may fail to capture variation in these traits. Litter chemical traits therefore provide a mechanistic link between organisms, species diversity, and key components of below-ground ecosystem function.

  8. Measures of School Integration: Comparing Coleman's Index to Measures of Species Diversity.

    Science.gov (United States)

    Mercil, Steven Bray; Williams, John Delane

    This study used species diversity indices developed in ecology as a measure of socioethnic diversity, and compared them to Coleman's Index of Segregation. The twelve indices were Simpson's Concentration Index ("ell"), Simpson's Index of Diversity, Hurlbert's Probability of Interspecific Encounter (PIE), Simpson's Probability of…

  9. Butterflies show different functional and species diversity in relationship to vegetation structure and land use

    NARCIS (Netherlands)

    Aguirre-Gutiérrez, J.; WallisDeVries, M.F.; Marshall, L.; van't Zelfde, M.; Villalobos-Arámbula, A.R.; Boekelo, B.; Bartholomeus, H.; Franzén, M.; Biesmeijer, J.C.

    2017-01-01

    Aim: Biodiversity is rapidly disappearing at local and global scales also affecting the functional diversity of ecosystems. We aimed to assess whether functional diversity was correlated with species diversity and whether both were affected by similar land use and vegetation structure drivers.

  10. Estimating tree species diversity in the savannah using NDVI and woody canopy cover

    Science.gov (United States)

    Madonsela, Sabelo; Cho, Moses Azong; Ramoelo, Abel; Mutanga, Onisimo; Naidoo, Laven

    2018-04-01

    Remote sensing applications in biodiversity research often rely on the establishment of relationships between spectral information from the image and tree species diversity measured in the field. Most studies have used normalized difference vegetation index (NDVI) to estimate tree species diversity on the basis that it is sensitive to primary productivity which defines spatial variation in plant diversity. The NDVI signal is influenced by photosynthetically active vegetation which, in the savannah, includes woody canopy foliage and grasses. The question is whether the relationship between NDVI and tree species diversity in the savanna depends on the woody cover percentage. This study explored the relationship between woody canopy cover (WCC) and tree species diversity in the savannah woodland of southern Africa and also investigated whether there is a significant interaction between seasonal NDVI and WCC in the factorial model when estimating tree species diversity. To fulfil our aim, we followed stratified random sampling approach and surveyed tree species in 68 plots of 90 m × 90 m across the study area. Within each plot, all trees with diameter at breast height of >10 cm were sampled and Shannon index - a common measure of species diversity which considers both species richness and abundance - was used to quantify tree species diversity. We then extracted WCC in each plot from existing fractional woody cover product produced from Synthetic Aperture Radar (SAR) data. Factorial regression model was used to determine the interaction effect between NDVI and WCC when estimating tree species diversity. Results from regression analysis showed that (i) WCC has a highly significant relationship with tree species diversity (r2 = 0.21; p NDVI and WCC is not significant, however, the factorial model significantly reduced the error of prediction (RMSE = 0.47, p NDVI (RMSE = 0.49) or WCC (RMSE = 0.49) model during the senescence period. The result justifies our assertion

  11. Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing

    Science.gov (United States)

    Chao, Yuanqing; Mao, Yanping; Wang, Zhiping; Zhang, Tong

    2015-06-01

    The development of biofilms in drinking water (DW) systems may cause various problems to water quality. To investigate the community structure of biofilms on different pipe materials and the global/specific metabolic functions of DW biofilms, PCR-based 454 pyrosequencing data for 16S rRNA genes and Illumina metagenomic data were generated and analysed. Considerable differences in bacterial diversity and taxonomic structure were identified between biofilms formed on stainless steel and biofilms formed on plastics, indicating that the metallic materials facilitate the formation of higher diversity biofilms. Moreover, variations in several dominant genera were observed during biofilm formation. Based on PCA analysis, the global functions in the DW biofilms were similar to other DW metagenomes. Beyond the global functions, the occurrences and abundances of specific protective genes involved in the glutathione metabolism, the SoxRS system, the OxyR system, RpoS regulated genes, and the production/degradation of extracellular polymeric substances were also evaluated. A near-complete and low-contamination draft genome was constructed from the metagenome of the DW biofilm, based on the coverage and tetranucleotide frequencies, and identified as a Bradyrhizobiaceae-like bacterium according to a phylogenetic analysis. Our findings provide new insight into DW biofilms, especially in terms of their metabolic functions.

  12. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

    KAUST Repository

    Neave, Matthew J.

    2017-01-17

    Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

  13. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

    KAUST Repository

    Neave, Matthew J.; Michell, Craig; Apprill, Amy; Voolstra, Christian R.

    2017-01-01

    Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

  14. Fish species diversity and conservation in Beijing and adjacent areas

    OpenAIRE

    Chunguang Zhang; Yahui Zhao; Yingchun Xing; Ruilu Guo; Qing Zhang; Yun Feng; Enyuan Fan

    2011-01-01

    Based on field surveys between 2002 and 2010, and fish collections in the National Zoological Museum, Institute of Zoology, Chinese Academy of Sciences, a total of 93 wild fish species including 12 in-troduced species had been recorded in Beijing and adjacent areas. Eighty five of these species, including some migratory and estuarine fishes, are native to the region. Only 43 native wild species were collected in our field work from 2002 to 2010. Compared with the historical records, nearly 50...

  15. Evaluating β Diversity as a Surrogate for Species Representation at Fine Scale.

    Directory of Open Access Journals (Sweden)

    Paul Beier

    Full Text Available Species turnover or β diversity is a conceptually attractive surrogate for conservation planning. However, there has been only 1 attempt to determine how well sites selected to maximize β diversity represent species, and that test was done at a scale too coarse (2,500 km2 sites to inform most conservation decisions. We used 8 plant datasets, 3 bird datasets, and 1 mammal dataset to evaluate whether sites selected to span β diversity will efficiently represent species at finer scale (sites sizes < 1 ha to 625 km2. We used ordinations to characterize dissimilarity in species assemblages (β diversity among plots (inventory data or among grid cells (atlas data. We then selected sites to maximize β diversity and used the Species Accumulation Index, SAI, to evaluate how efficiently the surrogate (selecting sites for maximum β diversity represented species in the same taxon. Across all 12 datasets, sites selected for maximum β diversity represented species with a median efficiency of 24% (i.e., the surrogate was 24% more effective than random selection of sites, and an interquartile range of 4% to 41% efficiency. β diversity was a better surrogate for bird datasets than for plant datasets, and for atlas datasets with 10-km to 14-km grid cells than for atlas datasets with 25-km grid cells. We conclude that β diversity is more than a mere descriptor of how species are distributed on the landscape; in particular β diversity might be useful to maximize the complementarity of a set of sites. Because we tested only within-taxon surrogacy, our results do not prove that β diversity is useful for conservation planning. But our results do justify further investigation to identify the circumstances in which β diversity performs well, and to evaluate it as a cross-taxon surrogate.

  16. BOX-PCR-based identification of bacterial species belonging to Pseudomonas syringae: P. viridiflava group

    Directory of Open Access Journals (Sweden)

    Abi S.A. Marques

    2008-01-01

    Full Text Available The phenotypic characteristics and genetic fingerprints of a collection of 120 bacterial strains, belonging to Pseudomonas syringae sensu lato group, P. viridiflava and reference bacteria were evaluated, with the aim of species identification. The numerical analysis of 119 nutritional characteristics did not show patterns that would help with identification. Regarding the genetic fingerprinting, the results of the present study supported the observation that BOX-PCR seems to be able to identify bacterial strains at species level. After numerical analyses of the bar-codes, all pathovars belonging to each one of the nine described genomospecies were clustered together at a distance of 0.72, and could be separated at genomic species level. Two P. syringae strains of unknown pathovars (CFBP 3650 and CFBP 3662 and the three P. syringae pv. actinidiae strains were grouped in two extra clusters and might eventually constitute two new species. This genomic species clustering was particularly evident for genomospecies 4, which gathered P. syringae pvs. atropurpurea, coronafaciens, garçae, oryzae, porri, striafaciens, and zizaniae at a noticeably low distance.

  17. A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

    Directory of Open Access Journals (Sweden)

    Glass John I

    2010-07-01

    Full Text Available Abstract Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT. Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Results Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the

  18. French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives

    Directory of Open Access Journals (Sweden)

    Guillaume eMinard

    2015-09-01

    Full Text Available The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the 21st century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype and bacterial diversity (16S rDNA metabarcoding were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects.

  19. Plaque bacterial microbiome diversity in children younger than 30 months with or without caries prior to eruption of second primary molars.

    Directory of Open Access Journals (Sweden)

    He Xu

    Full Text Available OBJECTIVE: Our primary objective is to phylogenetically characterize the supragingival plaque bacterial microbiome of children prior to eruption of second primary molars by pyrosequencing method for studying etiology of early childhood caries. METHODS: Supragingival plaque samples were collected from 10 caries children and 9 caries-free children. Plaque DNA was extracted, used to generate DNA amplicons of the V1-V3 hypervariable region of the bacterial 16S rRNA gene, and subjected to 454-pyrosequencing. RESULTS: On average, over 22,000 sequences per sample were generated. High bacterial diversity was noted in the plaque of children with caries [170 operational taxonomical units (OTU at 3% divergence] and caries-free children (201 OTU at 3% divergence with no significant difference. A total of 8 phyla, 15 classes, 21 orders, 30 families, 41 genera and 99 species were represented. In addition, five predominant phyla (Firmicute, Fusobacteria, Proteobacteria, Bacteroidetes and Actinobacteria and seven genera (Leptotrichia, Streptococcus, Actinomyces, Prevotella, Porphyromonas, Neisseria, and Veillonella constituted a majority of contents of the total microbiota, independent of the presence or absence of caries. Principal Component Analysis (PCA presented that caries-related genera included Streptococcus and Veillonella; while Leptotrichia, Selenomonas, Fusobacterium, Capnocytophaga and Porphyromonas were more related to the caries-free samples. Neisseria and Prevotella presented approximately in between. In both groups, the degree of shared organism lineages (as defined by species-level OTUs among individual supragingival plaque microbiomes was minimal. CONCLUSION: Our study represented for the first time using pyrosequencing to elucidate and monitor supragingival plaque bacterial diversity at such young age with second primary molar unerrupted. Distinctions were revealed between caries and caries-free microbiomes in terms of microbial community

  20. Conserving the stage: climate change and the geophysical underpinnings of species diversity.

    Directory of Open Access Journals (Sweden)

    Mark G Anderson

    Full Text Available Conservationists have proposed methods for adapting to climate change that assume species distributions are primarily explained by climate variables. The key idea is to use the understanding of species-climate relationships to map corridors and to identify regions of faunal stability or high species turnover. An alternative approach is to adopt an evolutionary timescale and ask ultimately what factors control total diversity, so that over the long run the major drivers of total species richness can be protected. Within a single climatic region, the temperate area encompassing all of the Northeastern U.S. and Maritime Canada, we hypothesized that geologic factors may take precedence over climate in explain