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Here, we report the genome sequence of Tenacibaculum mesophilum strain ECR, which was isolated from the river/ocean interface at Trunk River in Falmouth, Massachusetts. The isolation and sequencing were performed as part of the 2016 and 2018 Microbial Diversity courses at the Marine Biological Laboratory in Woods Hole, Massachusetts.

An anaerobic methanotroph (ANME-2d) can perform nitrate-driven anaerobic oxidation of methane through reverse methanogenesis, using nitrate as the terminal electron acceptor, and nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium. Anaerobic link for carbon and nitrogen cycles Microbes capable of the anaerobic oxidation of methane (AOM) are important for controlling the flux of methane from anoxic marine sediments. Recent work has demonstrated AOM coupled to sulphate reduction in a consortium of ANME (anaerobic methanotrophic archaea) and sulphate-reducing bacteria, and coupled to nitrite reduction in consortia enriched with the bacterium Candidatus Methylomirabilis oxyfera and the novel ANME-2d lineage. Here Gene Tyson and colleagues show that a novel ANME-2d archaeon, which they name Candidatus Methanoperedens nitroreducens, is able to performing nitrate-driven AOM without a partner organism via reverse methanogenesis with nitrate as the terminal electron acceptor, using genes for nitrate reduction that have been laterally transferred from a bacterial donor. The authors speculate that ANME- 2d or Methanoperedenaceae lineage may have a pivotal role in linking the global carbon and nitrogen cycles in anoxic environments. Anaerobic oxidation of methane (AOM) is critical for controlling the flux of methane from anoxic environments. AOM coupled to iron.sup.1, manganese.sup.1 and sulphate.sup.2 reduction have been demonstrated in consortia containing anaerobic methanotrophic (ANME) archaea. More recently it has been shown that the bacterium Candidatus'Methylomirabilis oxyfera' can couple AOM to nitrite reduction through an intra-aerobic methane oxidation pathway.sup.3. Bioreactors capable of AOM coupled to denitrification have resulted in the enrichment of 'M. oxyfera' and a novel ANME lineage, ANME-2d.sup.4,5. However, as 'M. oxyfera' can independently couple AOM to denitrification, the role of ANME-2d in the process is unresolved. Here, a bioreactor fed with nitrate, ammonium and methane was dominated by a single ANME-2d population performing nitrate-driven AOM. Metagenomic, single-cell genomic and metatranscriptomic analyses combined with bioreactor performance and .sup.13C- and .sup.15N-labelling experiments show that ANME-2d is capable of independent AOM through reverse methanogenesis using nitrate as the terminal electron acceptor. Comparative analyses reveal that the genes for nitrate reduction were transferred laterally from a bacterial donor, suggesting selection for this novel process within ANME-2d. Nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium, effectively outcompeting 'M. oxyfera' in the system. We propose the name Candidatus 'Methanoperedens nitroreducens' for the ANME-2d population and the family Candidatus'Methanoperedenaceae' for the ANME-2d lineage. We predict that 'M. nitroreducens' and other members of the 'Methanoperedenaceae' have an important role in linking the global carbon and nitrogen cycles in anoxic environments., Author(s): Mohamed F. Haroon [sup.1] , Shihu Hu [sup.2] , Ying Shi [sup.2] , Michael Imelfort [sup.1] [sup.2] , Jurg Keller [sup.2] , Philip Hugenholtz [sup.1] [sup.3] , Zhiguo Yuan [...]

Association mapping currently relies on the identification of genetic markers. Several technologies have been adopted for genetic marker analysis, with single nucleotide polymorphisms (SNPs) being the most popular where a reasonable quantity of genome sequence data are available. We describe several tools we have developed for the discovery, annotation, and visualization of molecular markers for association mapping. These include autoSNPdb for SNP discovery from assembled sequence data; TAGdb for the identification of gene specific paired read Illumina GAII data; CMap3D for the comparison of mapped genetic and physical markers; and BAC and Gene Annotator for the online annotation of genes and genomic sequences. Key words: SNP discovery, association mapping, comparative genomics, second generation genome sequencing. L'analyse d'association repose presentement sur l'identification de marqueurs genetiques. Plusieurs technologies ont ete employees pour l'analyse de marqueurs genetiques, les polymorphismes mononucleeotidiques (SNP) etant les plus populaires la oil une information genomique suffisante etait disponible. Les auteurs decrivent plusieurs outils qu'ils ont deeveloppees pour l'identification, l'annotation et la visualisation des marqueurs moleeculaires pour des fins d'analyse d'association. Ceux-ci incluent autoSNPdb pour l'identification de SNP au sein de donneees de sequence, TAGdb pour l'identification d'etiquettes specifiques d'un gene au sein de collections d'etiquettes de sequence Illumina GAII, CMap3D pour la comparaison de marqueurs genetiques et physiques, et un annotateur de clones BAC et de genes pour effectuer l'annotation automatiseedegenes et de sequences geenomiques. Mots-cles: identification de SNP, analyse d'association, genomique comparee, sequencjage genomique de seconde geeneration., Introduction Association mapping is being driven by changes in technology that permit the discovery of large numbers of genetic variants and the screening for these genetic variations across large populations. [...]

Abstract Background The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes. Results We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome. Conclusions The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly.

Nature 500, 567-570(2013); doi:10.1038/nature12375 In this Letter, equation (1) was inadvertently shown incorrectly, with C[O.sub.2] missing from the reaction products. The correct equation (1) is shown below: C[H.sub.4] + 4N[O.sup.-.sub.3] [...]