Chistoserdov Andrei Y.

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Andrei Y.

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  • Article
    Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities
    (BioMed Central, 2009-11-03) Stoeck, Thorsten ; Behnke, Anke ; Christen, Richard ; Amaral-Zettler, Linda A. ; Rodriguez-Mora, Maria J. ; Chistoserdov, Andrei Y. ; Orsi, William D. ; Edgcomb, Virginia P.
    Recent advances in sequencing strategies make possible unprecedented depth and scale of sampling for molecular detection of microbial diversity. Two major paradigm-shifting discoveries include the detection of bacterial diversity that is one to two orders of magnitude greater than previous estimates, and the discovery of an exciting 'rare biosphere' of molecular signatures ('species') of poorly understood ecological significance. We applied a high-throughput parallel tag sequencing (454 sequencing) protocol adopted for eukaryotes to investigate protistan community complexity in two contrasting anoxic marine ecosystems (Framvaren Fjord, Norway; Cariaco deep-sea basin, Venezuela). Both sampling sites have previously been scrutinized for protistan diversity by traditional clone library construction and Sanger sequencing. By comparing these clone library data with 454 amplicon library data, we assess the efficiency of high-throughput tag sequencing strategies. We here present a novel, highly conservative bioinformatic analysis pipeline for the processing of large tag sequence data sets.The analyses of ca. 250,000 sequence reads revealed that the number of detected Operational Taxonomic Units (OTUs) far exceeded previous richness estimates from the same sites based on clone libraries and Sanger sequencing. More than 90% of this diversity was represented by OTUs with less than 10 sequence tags. We detected a substantial number of taxonomic groups like Apusozoa, Chrysomerophytes, Centroheliozoa, Eustigmatophytes, hyphochytriomycetes, Ichthyosporea, Oikomonads, Phaeothamniophytes, and rhodophytes which remained undetected by previous clone library-based diversity surveys of the sampling sites. The most important innovations in our newly developed bioinformatics pipeline employ (i) BLASTN with query parameters adjusted for highly variable domains and a complete database of public ribosomal RNA (rRNA) gene sequences for taxonomic assignments of tags; (ii) a clustering of tags at k differences (Levenshtein distance) with a newly developed algorithm enabling very fast OTU clustering for large tag sequence data sets; and (iii) a novel parsing procedure to combine the data from individual analyses. Our data highlight the magnitude of the under-sampled 'protistan gap' in the eukaryotic tree of life. This study illustrates that our current understanding of the ecological complexity of protist communities, and of the global species richness and genome diversity of protists, is severely limited. Even though 454 pyrosequencing is not a panacea, it allows for more comprehensive insights into the diversity of protistan communities, and combined with appropriate statistical tools, enables improved ecological interpretations of the data and projections of global diversity.
  • Article
    Culture-dependent characterization of the microbial community associated with epizootic shell disease lesions in American lobster, Homarus americanus
    (National Shellfisheries Association, 2005-10-01) Chistoserdov, Andrei Y. ; Smolowitz, Roxanna M. ; Mirasol, Feliza ; Hsu, Andrea
    Epizootic shell disease in the American lobster is an important factor affecting lobster fisheries in and around the Long Island Sound. It is a strictly dermal disease, because no correlation was observed between occurrence of epizootic shell disease and hemolymph infection. The culturability of bacteria from lesions was variable and averaged around 1.1%. The lesions contained two to four orders of magnitude more bacteria than healthy carapace surfaces of the same animal. Chitinoclastic bacteria comprised a very small fraction of bacteria present in the lesions, suggesting that their role in epizootic shell disease may be limited. Phylogenetic analysis of bacteria isolated from the lesions showed no typical bacterial pathogens of lobsters such as Aerococcus viridans or Vibrio fluvialis. Moreover, bacteria commonly associated with shell disease of other Crustacea or other forms of shell disease of the American lobster were not found. Two common groups of bacteria were isolated from lesions of all lobsters used in this research: one belonging to a species complex affiliated with the Flavobacteriaceae family and the second belonging to a series of closely related if not identical strains of Pseudoalteromonas gracilis. Bacteria isolated from only a few lobsters were related to Shewanella frigidimarina, Alteromonas arctica, Vibrio lentus, Shewanella fidelia, Pseudoalteromonas tunicata and Vibrio spp. Based on the analyses of culturable isolates, overall microbial communities found in lesions of lobsters from eastern Long Island Sound and Buzzards Bay appear to be similar to each other.
  • Article
    The diversity of sulfide oxidation and sulfate reduction genes expressed by the bacterial communities of the Cariaco Basin, Venezuela
    (Bentham Open, 2016-08-31) Rodriguez-Mora, Maria J. ; Edgcomb, Virginia P. ; Taylor, Craig D. ; Scranton, Mary I. ; Taylor, Gordon T. ; Chistoserdov, Andrei Y.
    Qualitative expression of dissimilative sulfite reductase (dsrA), a key gene in sulfate reduction, and sulfide:quinone oxidoreductase (sqr), a key gene in sulfide oxidation was investigated. Neither of the two could be amplified from mRNA retrieved with Niskin bottles but were amplified from mRNA retrieved by the Deep SID. The sqr and sqr-like genes retrieved from the Cariaco Basin were related to the sqr genes from a Bradyrhizobium sp., Methylomicrobium alcaliphilum, Sulfurovum sp. NBC37-1, Sulfurimonas autotrophica, Thiorhodospira sibirica and Chlorobium tepidum. The dsrA gene sequences obtained from the redoxcline of the Cariaco Basin belonged to chemoorganotrophic and chemoautotrophic sulfate and sulfur reducers belonging to the class Deltaproteobacteria (phylum Proteobacteria) and the order Clostridiales (phylum Firmicutes).