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      Comparison of bacterial diversity in full scale anammox bioreactors operated under different conditions

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          NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes

          Microbiologists conducting surveys of bacterial and archaeal diversity often require comparative alignments of thousands of 16S rRNA genes collected from a sample. The computational resources and bioinformatics expertise required to construct such an alignment has inhibited high-throughput analysis. It was hypothesized that an online tool could be developed to efficiently align thousands of 16S rRNA genes via the NAST (Nearest Alignment Space Termination) algorithm for creating multiple sequence alignments (MSA). The tool was implemented with a web-interface at . Each user-submitted sequence is compared with Greengenes' ‘Core Set’, comprising ∼10 000 aligned non-chimeric sequences representative of the currently recognized diversity among bacteria and archaea. User sequences are oriented and paired with their closest match in the Core Set to serve as a template for inserting gap characters. Non-16S data (sequence from vector or surrounding genomic regions) are conveniently removed in the returned alignment. From the resulting MSA, distance matrices can be calculated for diversity estimates and organisms can be classified by taxonomy. The ability to align and categorize large sequence sets using a simple interface has enabled researchers with various experience levels to obtain bacterial and archaeal community profiles.
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            454 pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants.

            Activated sludge (AS) contains highly complex microbial communities. In this study, PCR-based 454 pyrosequencing was applied to investigate the bacterial communities of AS samples from 14 sewage treatment plants of Asia (mainland China, Hong Kong, and Singapore), and North America (Canada and the United States). A total of 259 K effective sequences of 16S rRNA gene V4 region were obtained from these AS samples. These sequences revealed huge amount of operational taxonomic units (OTUs) in AS, that is, 1183-3567 OTUs in a sludge sample, at 3% cutoff level and sequencing depth of 16,489 sequences. Clear geographical differences among the AS samples from Asia and North America were revealed by (1) cluster analyses based on abundances of OTUs or the genus/family/order assigned by Ribosomal Database Project (RDP) and (2) the principal coordinate analyses based on OTUs abundances, RDP taxa abundances and UniFrac of OTUs and their distances. In addition to certain unique bacterial populations in each AS sample, some genera were dominant, and core populations shared by multiple samples, including two commonly reported genera of Zoogloea and Dechloromonas, three genera not frequently reported (i.e., Prosthecobacter, Caldilinea and Tricoccus) and three genera not well described so far (i.e., Gp4 and Gp6 in Acidobacteria and Subdivision3 genera incertae sedis of Verrucomicrobia). Pyrosequencing analyses of multiple AS samples in this study also revealed the minority populations that are hard to be explored by traditional molecular methods and showed that a large proportion of sequences could not be assigned to taxonomic affiliations even at the phylum/class levels.
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              Startup of reactors for anoxic ammonium oxidation: experiences from the first full-scale anammox reactor in Rotterdam.

              The first full-scale anammox reactor in the world was started in Rotterdam (NL). The reactor was scaled-up directly from laboratory-scale to full-scale and treats up to 750 kg-N/d. In the initial phase of the startup, anammox conversions could not be identified by traditional methods, but quantitative PCR proved to be a reliable indicator for growth of the anammox population, indicating an anammox doubling time of 10-12 days. The experience gained during this first startup in combination with the availability of seed sludge from this reactor, will lead to a faster startup of anammox reactors in the future. The anammox reactor type employed in Rotterdam was compared to other reactor types for the anammox process. Reactors with a high specific surface area like the granular sludge reactor employed in Rotterdam provide the highest volumetric loading rates. Mass transfer of nitrite into the biofilm is limiting the conversion of those reactor types that have a lower specific surface area. Now the first full-scale commercial anammox reactor is in operation, a consistent and descriptive nomenclature is suggested for reactors in which the anammox process is employed.
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                Author and article information

                Journal
                Biotechnology Progress
                Biotechnol Progress
                Wiley
                87567938
                November 2015
                November 2015
                August 25 2015
                : 31
                : 6
                : 1464-1472
                Affiliations
                [1 ]Dept. of Civil Engineering; University of Granada; Campus De Fuentenueva, S/N Granada 18701 Spain
                [2 ]Inst. of Water Research, University of Granada; C/Ramón y Cajal, 4 Granada 18701 Spain
                [3 ]Dept. of Biotechnology; Technical University of Delft; Julianalaan 67 Delft 2628 BC The Netherlands
                Article
                10.1002/btpr.2151
                26260060
                b1ab4be3-36c2-4518-b22f-b3e77bb19ad1
                © 2015

                http://doi.wiley.com/10.1002/tdm_license_1.1

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