Spatio-temporal variability in ammonia oxidation and ammonia oxidising bacteria and archaea in coastal sediments of the Western English Channel

The abundance of ammonia-oxidising bacterial (AOB) and ammonia-oxidising archaeal (AOA) (amoA) genes and ammonia oxidation rates were compared bimonthly from July 2008 to May 2011 in 4 contrasting coastal sediments in the western English Channel. Despite a higher abundance of AOA amoA genes within all sediments and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Sediment type was a major factor in determining both AOB amoA gene abundance and AOB community structure, possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation. Decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. PCR-DGGE of AOB amoA genes indicated that no seasonal changes to community composition occurred; however, a gradual movement in community composition occurred at 3 of the sites studied. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rates, or any other environmental variable measured, may be related to the higher spatial variation amongst measurements, obscuring temporal trends, or the bimonthly sampling, which may have been too infrequent to capture temporal variability in the deposition of fresh organic matter. Alternatively, AOA may respond to changing substrate concentrations by an increase or decrease in transcript rather than gene abundance.

Disturbance to conserved bacterial communities in the cold water gorgonian coral Eunicella verrucosa

The bacterial communities associated with healthy and diseased colonies of the cold-water gorgonian coral Eunicella verrucosa at three sites off the south-west coast of England were compared using denaturing gradient gel electrophoresis (DGGE) and clone libraries. Significant differences in community structure between healthy and diseased samples were discovered, as were differences in the level of disturbance to these communities at each site; this correlated with depth and sediment load. The majority of cloned sequences from healthy coral tissue affiliated with the Gammaproteobacteria. The stability of the bacterial community and dominance of specific genera found across visibly healthy colonies suggest the presence of a specific microbial community. Affiliations included a high proportion of Endozoicomonas sequences, which were most similar to sequences found in tropical corals. This genus has been found in a number of invertebrates and is suggested to have a role in coral health and in the metabolisation of dimethylsulfoniopropionate (DMSP) produced by zooxanthellae. However, screening of colonies for the presence of zooxanthellae produced a negative result. Diseased colonies showed a decrease in affiliated clones and an increase in clones related to potentially harmful/transient microorganisms but no increase in a particular pathogen. This study demonstrates that a better understanding of these bacterial communities, the factors that affect them and their role in coral health and disease will be of critical importance in predicting future threats to temperate gorgonian communities.

Dynamic responses of the benthic bacterial community at the Western English Channel observatory site L4 are driven by deposition of fresh phytodetritus

The impact of the seasonal deposition of phytoplankton and phytodetritus on surface sediment bacterial abundance and community composition was investigated at the Western English Channel site L4. Sediment and water samples were collected from January to September in 2012, increasing in frequency during periods of high water column phytoplankton abundance. Compared to the past two decades, the spring bloom in 2012 was both unusually long in duration and contained higher than average biomass. Within spring months, the phytoplankton bloom was well mixed through the water column and showed accumulations near the sea bed, as evidenced by flow cytometry measurements of nanoeukaryotes, water column chlorophyll a and the appearance of pelagic phytoplankton at the sediment. Measurements of chlorophyll and chlorophyll degradation products indicated phytoplankton material was heavily degraded after it reached the sediment surface: the nature of the chlorophyll degradation products (predominantly pheophorbide, pyropheophorbide and hydroxychlorophyllone) was indicative of grazing activity. The abundance of bacterial 16S rRNA genes g−1 sediment (used as a proxy for bacterial biomass) increased markedly with the onset of the phytoplankton bloom, and correlated with measurements of chlorophyll at the surface sediment. Together, this suggests that bacteria may have responded to nutrients released via grazing activity. In depth sequencing of the 16S rRNA genes indicated that the composition of the bacterial community shifted rapidly through-out the prolonged spring bloom period. This was primarily due to an increase in the relative sequence abundance of Flavobacteria.