Spatio-temporal variability and diversity of water column prokaryotic communities in the eastern North Atlantic.

This work describes the microbial community structure in the water column at the Porcupine Abyssal Plain in the eastern North Atlantic. Restriction fragment length polymorphism analysis was carried out on clone libraries constructed from samples collected at 100 m, 1000 m, 3000 m, 10 m above bottom and sediment contact water during July 1997 and March 1998. Simpson (1/D) and Shannon (H') diversity indices revealed temporal and spatial variations in the community structure and complexity. Higher diversity was observed in the samples collected from 100 m (H'=3.22), 1000 m (H'=3.48) and 10 m above bottom (H'=3.18) during July 1997 compared with the corresponding samples during March 1998. Changes in diversity may be associated with a seasonal flux in particulate organic matter. This could promote the proliferation of a selection of taxa that are adapted to rapidly responding to a large influx of organic matter. Sequencing of clones representing 20 operational taxonomic units revealed a diverse population of Bacteria and Archaea. The most numerous clone operational taxonomic units were from the alpha and gamma subdivisions of the Proteobacteria and the group I marine Crenarchaeota. A number of sequences were phylogenetically grouped in clades with no culture representatives such as the SAR116, SAR86, SAR406 and SAR324 groups. Most of the sequences identified were found to be more closely related to other 16S rDNA clones recovered from the marine environment rather than cultured species.

Microbial community structure and methanogenic activity during start-up of psychrophilic anaerobic digesters treating synthetic industrial wastewaters.

Culture-independent, molecular techniques were applied to the characterization of microbial communities of an anaerobic granular sludge obtained from a full-scale digester. Procedures were optimised for total DNA recovery and polymerase chain reaction (PCR) amplification of 16S rDNA using archaea- and eubacteria-specific oligonucleotide primers. Cloned PCR products were subsequently screened by amplified rDNA restriction analysis to identify operational taxonomic units (OTUs). Inserts from clones representing each OTU were sequenced and phylogenetic trees were prepared. In addition, the microbial communities were characterised using terminal restriction fragment length polymorphism (T-RFLP). The specific methanogenic activity of the biomass, against various substrates, was also ascertained. Two anaerobic bioreactors were seeded with granular and non-granular (i.e. crushed) aliquots of the characterised sludge, respectively, and used to investigate the treatment of a volatile fatty acid (VFA)-based synthetic wastewater, at a loading rate of 5 kg COD m(-3) day(-1) at low ambient temperatures (18 degrees C). DNA was isolated from sludge samples during the test period and shifts in archaeal and eubacterial population structures were elucidated. The start-up period was successful with methane yields and COD removal efficiencies of 60-75% and 65-85%, respectively. Specific methanogenic activities of reactor biomass, obtained at the conclusion of the trial, indicated the development of psychrotolerant biomass during the 90-day experiment. Furthermore, the efficacy of T-RFLP as a molecular tool for use in the surveyance of engineered ecosystems was confirmed.

Cyclin-dependent kinase 8 is expressed both maternally and zygotically during zebrafish embryo development.

Cyclin-dependent kinase 8 (cdk8) regulates transcription by phosphorylating RNA polymerase II and TFIIH. The mechanism of zygotic transcription activation during vertebrate embryonic development is poorly understood. Here we describe the cloning and developmental expression pattern of zebrafish cdk8 mRNA. It is highly conserved, sharing 79% DNA and 95% amino acid sequence identity with human cdk8, thereby indicating an important role for the protein. Northern blotting and whole mount in situ hybridisation revealed expression of zebrafish cdk8 maternally, following the onset of zygotic transcription at the mid-blastula transition (MBT) and throughout embryonic development.