Publications

4477

Termites harbor diverse symbiotic gut microorganisms, the majority of which are as yet uncultivable and their interrelationships unclear. Here, we present the complete genome sequence of the uncultured Bacteroidales endosymbiont of the cellulolytic protist Pseudotrichonympha grassii, which accounts for 70% of the bacterial cells in the gut of the termite Coptotermes formosanus . Functional annotation of the chromosome (1,114,206 base pairs) unveiled its ability to fix dinitrogen and recycle putative host nitrogen wastes for biosynthesis of diverse amino acids and cofactors, and import glucose and xylose as energy and carbon sources. Thus, nitrogen fixation and cellulolysis are coupled within the protist's cells. This highly evolved symbiotic system probably underlies the ability of the worldwide pest termites Coptotermes to use wood as their sole food.

A new ‘Candidatus Liberibacter’ species was recently identified in tomato, capsicum, and potato in New Zealand. The tomato/potato psyllid, Bactericera cockerelli, is thought to be the vector of this species of liberibacter. During studies to determine additional host plants of the pathogen, leaves of Solanum betaceum (tamarillo, also known as tree tomato) and leaves and stems of Physalis peruviana (cape gooseberry) were collected from a home garden in South Auckland, New Zealand in July of 2008. These plants were not showing any obvious disease symptoms. They were located close to a commercial glasshouse site containing known liberibacter-infected tomatoes, and many psyllids were observed on the tamarillo tree over the summer and until late autumn. Total DNA was extracted from four tamarillo and two cape gooseberry samples with a DNeasy Plant Mini Kit (Qiagen, Valencia, CA). Samples from tamarillo that were used for the extraction were taken from the midveins of old and young leaves and from young petioles. For cape gooseberry, samples were from the leaf midveins and the stems. The samples were tested by PCR using primers OA2 (GenBank Accession No. EU834130) and OI2c (1). These primers amplify a 1,160-bp fragment of the 16S rRNA gene of the new liberibacter species. Amplicons of the expected size were obtained from all four tamarillo samples, with no amplification from negative control tamarillo plants grown from seed in an insect-proof glasshouse. Almost the entire length of the 16S rRNA gene was amplified using primer pairs fD2 (3)/OI2c and OA2/rP1 (3), and the 16S-23S rRNA intergenic spacer was amplified with primer pair OI2/23S1 (2). These amplicons, along with that from the OA2/OI2c primer pair, were directly sequenced, and overlapping fragments were assembled using the SeqMan software of the LaserGene package (DNASTAR, Inc., Madison, WI) (GenBank Accession No. EU935004). A 650-bp fragment of the β operon was also amplified and sequenced directly (GenBank Accession No. EU935005). BLAST analysis showed 100% nt identity to the liberibacter of tomato (GenBank Accession Nos. EU834130 and EU834131) and potato (GenBank Accession Nos. EU849020 and EU919514). The two cape gooseberry samples produced amplicons of the expected size with the 16S rRNA and β operon primers and the origin of the fragments were confirmed by direct sequencing with BLAST analysis showing 100% nt identity to isolates from tomato, potato, and tamarillo. To determine the distribution of disease, 53 samples of 10 leaves each (representing two leaves from five plants) were collected randomly from a commercial tamarillo crop in South Auckland. Small sections of the midveins were removed from each of the 10 leaves, bulked, and DNA was extracted as described above. The samples were tested by PCR using primer pair OA2/OI2c. Amplicons of the expected size were obtained from 2 of the 53 samples. To our knowledge, this is the first report of a liberibacter in tamarillo and cape gooseberry. It is unknown if the liberibacter induces symptoms in these species or if they act as symptomless reservoirs of the pathogen. The infected plants will be observed for symptom development over the course of a growing season. References: (1) S. Jagoueix et al. Mol. Cell. Probes 10:43, 1996. (2) S. Jagoueix et al. Int. J. Syst. Bacteriol. 47:224, 1997. (3) W. G. Weisburg et al. J. Bacteriol. 173:697, 1991.

DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator , composes >99.9% of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent life-style well suited to long-term isolation from the photosphere deep within Earth's crust and offers an example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.

Summary Members of the uncultured bacterial genus Candidatus Accumulibacter are capable of intracellular accumulation of inorganic phosphate in activated sludge wastewater treatment plants (WWTPs) performing enhanced biological phosphorus removal, but were also recently shown to inhabit freshwater and estuarine sediments. Additionally, metagenomic sequencing of two bioreactor cultures enriched in Candidatus Accumulibacter, but housed on separate continents, revealed the potential for global dispersal of particular Candidatus Accumulibacter strains, which we hypothesize is facilitated by the ability of Candidatus Accumulibacter to persist in environmental habitats. In the current study, we used sequencing of a phylogenetic marker, the ppk 1 gene, to characterize Candidatus Accumulibacter populations in diverse environments, at varying distances from WWTPs. We discovered several new lineages of Candidatus Accumulibacter which had not previously been detected in WWTPs, and also uncovered new diversity and structure within previously detected lineages. Habitat characteristics were found to be a key determinant of Candidatus Accumulibacter lineage distribution while, as predicted, geographic distance played little role in limiting dispersal on a regional scale. However, on a local scale, enrichment of particular Candidatus Accumulibacter lineages in WWTP appeared to impact local environmental populations. These results provide evidence of ecological differences among Candidatus Accumulibacter lineages.