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See detailAssessment of bioinformatic pipelines for the analysis of 454 pyrosequencing data using artificial cyanobacterial communities
Stelmach Pessi, Igor ULg; De Carvalho Maalouf, Pedro; Laughinghouse IV, Haywood ULg et al

Poster (2013, November 27)

The field of microbial ecology has undergone a revolution with the advent of next-generation sequencing (NGS) technologies, which revealed a higher microbial diversity than what was previously observed ... [more ▼]

The field of microbial ecology has undergone a revolution with the advent of next-generation sequencing (NGS) technologies, which revealed a higher microbial diversity than what was previously observed. The possibility of analyzing tens to hundreds of thousands sequences in a single sequencing run has provided information on rare taxa that could constitute an important fraction of microbial communities. However, this comes with the cost of relatively high error rates for individual reads, which can lead to overestimation of diversity due to the generation of spurious Operational Taxonomic Units (OTUs) consisting of erroneous sequences. Therefore, a correct assessment of microbial diversity using NGS relies on robust bioinformatic tools in order to correct for PCR and sequencing biases. Here we report on community structures recovered for two artificial cyanobacterial communities applying three commonly used and two recently published bioinformatic pipelines. This pilot study was made in the frame of the BELSPO project CCAMBIO. Artificial communities were constructed using DNA isolated from 22 cyanobacterial strains from the BCCM/ULC Polar Cyanobacteria Collection (http://bccm.belspo.be/about/ulc.php). DNA was extracted from individual cultures and pooled at equal (community Art1) or tiered (community Art2) concentrations. The V3-V4 hypervariable region of the 16S rRNA gene was amplified by PCR using primers 359F and 781Ra/781Rb [Nübel et al (1997) Appl Environ Microbiol 63: 3327-3332], and amplicons were sequenced on a 454 GS FLX Titanium platform. Data was demultiplexed and submitted to five bioinformatic pipelines for quality control of reads, removal of chimeric sequences and Operational Taxonomic Units (OTUs) clustering: (I) “shhh.flows (450 flows)”, (II) “shhh.flows (360-720 flows)” and (III) “Sliding Window (Q35, 50 bp)”, using MOTHUR according to Schloss et al (2011) [Schloss et al (2011) PLOS One 6: e27310]; (IV) “fastq_maxee” and (V) “fastq_truncqual”, using UPARSE according to Edgar (2013) [Edgar (2013) Nat Methods 10: 996-998]. Average sequence length varied considerably among pipelines, with pipeline I generating shorter reads (220 bp in average) and pipelines IV and V longer reads (370 bp). The number of OTUs obtained in each pipeline also varied significantly. While 22 and 21 OTUs were obtained for pipelines IV and V, respectively, pipelines I-III generated a surprisingly high number of OTUs (199, 317 and 289, respectively). Despite differences in the number of OTUs, the relative abundance of each reference strain did not differ significantly between pipelines. Overall, community structures observed using the UPARSE protocol (pipelines IV and V) were the most consistent with the expected results. These findings show the importance of assessing the performance of different bioinformatic pipelines using artificial communities, in order to reduce the effects of PCR and sequencing errors, which can lead to distorted community structures estimates. [less ▲]

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See detailBioregionalisation and biodiversity of Cyanobacterial communities in East- Antarctic lakes
De Carvalho Maalouf, Pedro ULg; Stelmach Pessi, Igor ULg; Verleyen, Elie et al

Poster (2013, July)

On the Antarctic continent, ice-free regions represent only 0.3% of the total surface area. In these regions, cyanobacteria are one of the dominant phototrophs and primary producers, forming cohesive ... [more ▼]

On the Antarctic continent, ice-free regions represent only 0.3% of the total surface area. In these regions, cyanobacteria are one of the dominant phototrophs and primary producers, forming cohesive benthic mats in lakes and other aquatic habitats. Using a recent compilation of published biodiversity data from Antarctica and the sub-Antarctic islands in combination with physical factors and expert-defined bioregions, Terauds et al. (2012) identified 15 biologically distinct ice-free Antarctic Conservation Biogeographic Regions (ACBRs). However, the degree and nature of bioregionalisation in Antarctic cyanobacterial communities is still largely unknown. In this study, cyanobacterial diversity was analysed using Denaturating Gradient Gel Electrophoresis (DGGE) on a partial 16S rRNA sequence (ca 400 bp) in 50 microbial mats originating from five of the seven ACBRs identified in East Antarctica. Comparison of the sequences with those available in GenBank was carried out to assess the geographical distribution of the taxa on both local and global scales. A total of 35 Operational Taxonomic Units (OTUs, group of sequences with more than 98.5% sequence similarity) was obtained for all samples. Moreover, the taxonomic turnover between the five ACBRs was relatively low, as 69.5% of the OTUs were present in 2 or 3 bioregions. Consistent with previous findings, a large proportion (37%) of the OTUs was restricted to the “cold biosphere”, and 17% appeared potentially endemic to the Antarctic continent. These results suggest that the patterns of bioregionalisation in East Antarctic cyanobacteria are different than the ACBR scheme. Therefore, it would be useful to study the microbial bioregionalisation in more detail and using less conserved molecular taxonomic markers than the 16S rRNA gene, such as the ITS region. Moreover, since DGGE only provides information on the dominant taxa in microbial assemblages, a high-throughput screening is currently being performed. [less ▲]

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See detailHuman impacts on Antarctic ecosystems: do not forget the microorganisms!
Hughes, Kevin; Verleyen, Elie; Vyverman, Wim et al

Conference (2013, July)

The tiny and microscopic creatures that are the permanent inhabitants of the Antarctic continent are often overlooked in environmental impact assessments and when new management and protection strategies ... [more ▼]

The tiny and microscopic creatures that are the permanent inhabitants of the Antarctic continent are often overlooked in environmental impact assessments and when new management and protection strategies are designed. This lack of consideration is probably due to their small size and the need of sophisticated molecular methods to study their diversity, evolution and geographic distribution. However, considerable progress has been made in the field of molecular diversity in the last two decennia, and is still ongoing for Antarctic bacteria, cyanobacteria, protists, fungi, etc. Recent studies have shown the presence of highly diverse microbial communities and the existence of species endemic to Antarctic in some taxonomic groups. With the emergence of High Throughput Sequencing methodologies that are able to detect ‘rare’ taxa, it becomes crucial to find Antarctic locations that have not yet been impacted by human presence. These ‘pristine’ areas are essential to serve as reference sites and allow to distinguish the true Antarctic organisms from the imported ones. Indeed, recent studies have shown that humans unintentionally disperse their own microbial flora but may also spread organisms from other locations. In the extreme biotopes with a reduced diversity that are currently found in Antarctica, such contaminations might have a profound impact. It is important to raise the awareness of scientists, environmental managers and policy makers about the necessity to single out some areas that are kept untouched, or where stringent biosecurity measures are taken. The purpose is not to hinder scientific research, but to weigh carefully, when exploring a new area, the importance of the acquired piece of knowledge in relation to the possibility of hindering future microbiological research. Some parallels with other fields of research are interesting to consider. Archeologists are used to keeping some parts of the explored caves untouched because they foresee that technological progress will allow better analyses in future. The COSPAR Panel on Planetary Protection makes recommendations to avoid the contamination of other planets with microbes from Earth, which would obscure any discovery of extraterrestrial indigenous life forms. These examples illustrate the essential need to integrate the delineation of reference areas for future analyses in the design and execution of scientific research. In fact, the Madrid Protocol foresees the possibility to designate ‘inviolate areas’ (Annex V, Article 3), though this tool has rarely been used. It would be useful if scientists of all disciplines would reflect how to use this management option. [less ▲]

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See detailNovel Bacterial Isolate from Permian Groundwater, Capable of Aggregating Potential Biofuel-Producing Microalga Nannochloropsis oceanica IMET1
Wang, H; Laughinghouse IV, Haywood ULg; Anderson, MA et al

in Applied and Environmental Microbiology (2012), 78(5), 1445-1453

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See detailPollen grain viability in accessions of Crotalaria juncea L. (Fabaceae)
Coelho, APD; Morais, K; Laughinghouse IV, Haywood ULg et al

in Agrociencia (2012), 46

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See detailPollen viability of Polygala paniculata L. (Polygalaceae) using different methods of staining
Frescura, VDS; Laughinghouse IV, Haywood ULg; Canto-Dorow, TS et al

in Biocell (2012), 36(3), 143-145

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See detailAntiproliferative effect of the arboreal and medicinal species Luehea divaricata on the Allium cepa cell cycle
Frescura, VDS; Laughinghouse IV, Haywood ULg; Tedesco, SB

in Caryologia : Giornale di Citologia, Citosistematica, e Citogenetica (2012), 65(1), 27-33

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See detailBioindicator of Genotoxicity: the Allium cepa test
Tedesco, S; Laughinghouse IV, Haywood ULg

in Srivastava, J.K. (Ed.) Environmental Contamination (2012)

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See detailA new red colonial Pseudanabaena (Cyanoprokaryota, Oscillatoriales) from North American large lakes
Kling, H; Laughinghouse IV, Haywood ULg; Smarda, J et al

in Fottea (Praha) (2012), 12(2), 327-339

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See detailBiomonitoring genotoxicity and cytotoxicity of Microcystis aeruginosa (Chroococcales, Cyanobacteria) using the Allium cepa test
Laughinghouse IV, Haywood ULg; Pra, D; Silva-Stenico, ME et al

in Science of the Total Environment (2012), 432

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See detailPollen viability of genotypes of Eragrostis plana from different geographic populations in Rio Grande do Sul, Brazil
Piccini, F; Frescura, VDS; Laughinghouse IV, Haywood ULg et al

in Enciclopédia Biosfera (2012), 8(15), 1316-1324

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See detailCharacterization of a novel freshwater gigartinalean red alga from Belize, with description of Sterrocladia belizeana sp. nov
Sherwood, AR; Necchi Jr, O; Carlile, AL et al

in Phycologia (2012), 51(6), 627-635

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See detailSeasonal productivity of a periphytic algal community for biofuel feedstock generation and nutrient treatment
Sandefur, HN; Matlock, MD; Costello, TA et al

in Ecological Engineering (2011), 37

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See detailABA-mediated proline synthesis in cowpea leaves exposed to water deficiency and rehydration
Costa, RCL; Lobato, AKS; Silveira, JAG et al

in Turkish Journal of Agriculture & Forestry (2011), 35

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See detailSeed and Seedling Anatomy in Euterpe oleraceae Mart. during the Germination Process
Neto, MAM; Lobato, AKS; Alves, JD et al

in Journal of Food, Agriculture and Environment [=JFAE] (2010), 8(2), 1147-1152

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See detailAntiproliferative and genotoxic effects of Mikania glomerata (Asteraceae)
Dalla Nora, G; Pastori, T; Laughinghouse IV, Haywood ULg et al

in Biocell : Official Journal of the Sociedades Latinoamericanas de Microscopia Electronica ... Et. Al (2010), 34(3), 95-101

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See detailAlterations in the mitotic index of Allium cepa induced by infusions of Pluchea sagittalis submitted to three different cultivation systems
Rossato, LV; Tedesco, SB; Laughinghouse IV, Haywood ULg et al

in Anais da Academia Brasileira de Ciencias (2010), 82(4), 857-860

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See detailGenotoxic potential of aqueous extracts of Artemisia verlotorum on the cell cycle of Allium cepa
Souza, LFB; Laughinghouse IV, Haywood ULg; Pastori, T et al

in International Journal of Environmental Studies (2010), 67(6), 871-877

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