Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms

The impact of ocean acidification and carbonation on microbial community structure was assessed during a large-scale in situ costal pelagic mesocosm study, included as part of the EPOCA 2010 Arctic campaign. The mesocosm experiment included ambient conditions (fjord) and nine mesocosms with pCO(2) levels ranging from similar to 145 to similar to 1420 mu atm. Samples for the present study were collected at ten time points (t-1, t1, t5, t7, t12, t14, t18, t22, t26 to t28) in seven treatments (ambient fjord (similar to 145), 2x similar to 185, similar to 270, similar to 685, similar to 820, similar to 1050 mu atm) and were analysed for "small" and "large" size fraction microbial community composition using 16S rRNA (ribosomal ribonucleic acid) amplicon sequencing. This high-throughput sequencing analysis produced similar to 20 000 000 16S rRNA V4 reads, which comprised 7000OTUs. The main variables structuring these communities were sample origins (fjord or mesocosms) and the community size fraction (small or large size fraction). The community was significantly different between the unenclosed fjord water and enclosed mesocosms (both control and elevated CO2 treatments) after nutrients were added to the mesocosms, suggesting that the addition of nutrients is the primary driver of the change in mesocosm community structure. The relative importance of each structuring variable depended greatly on the time at which the community was sampled in relation to the phytoplankton bloom. The sampling strategy of separating the small and large size fraction was the second most important factor for community structure. When the small and large size fraction bacteria were analysed separately at different time points, the only taxon pCO(2) was found to significantly affect were the Gammaproteobacteria after nutrient addition. Finally, pCO(2) treatment was found to be significantly correlated (non-linear) with 15 rare taxa, most of which increased in abundance with higher CO2.

Minor impact of ocean acidification to the composition of the active microbial community in an Arctic sediment

Effects of ocean acidification on the composition of the active bacterial and archaeal community within Arctic surface sediment was analysed in detail using 16S rRNA 454 pyrosequencing. Intact sediment cores were collected and exposed to one of five different pCO(2) concentrations [380 (present day), 540, 750, 1120 and 3000 atm] and RNA extracted after a period of 14 days exposure. Measurements of diversity and multivariate similarity indicated very little difference between pCO(2) treatments. Only when the highest and lowest pCO(2) treatments were compared were significant differences evident, namely increases in the abundance of operational taxonomic units most closely related to the Halobacteria and differences to the presence/absence structure of the Planctomycetes. The relative abundance of members of the classes Planctomycetacia and Nitrospira increased with increasing pCO(2) concentration, indicating that these groups may be able to take advantage of changing pH or pCO(2) conditions. The modest response of the active microbial communities associated with these sediments may be due to the low and fluctuating pore-water pH already experienced by sediment microbes, a result of the pH buffering capacity of marine sediments, or due to currently unknown factors. Further research is required to fully understand the impact of elevated CO2 on sediment physicochemical parameters, biogeochemistry and microbial community dynamics.

Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments

In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal patterns in burrow sediments in comparison with surface sediments, suggesting that the burrow provides a unique environment where bacterial gene abundances are influenced directly by macrofaunal activity. In contrast, the abundances of archaeal ammonia oxidizers varied temporally but were not affected by bioturbation, indicating differential responses between bacterial and archaeal ammonia oxidizers to environmental physicochemical controls. This study highlights the importance of bioturbation as a control over the temporal variation in nitrogen-cycling microbial community dynamics within coastal sediments.

Spatial Variability of Durum Wheat Yield as Related to Soil Parameters in an Organic Field

The yield in organic farming is generally much lower than its potential, which is due to its specificity. The objective of the present study was to quantify the yield spatial variation of wheat and relate it to soil parameters in an organic farm located in the north of the Negev Desert. Soil samples were gathered in a triangular grid at three time intervals. Yields were measured at 73 georeferenced points before the actual harvest. Several thematic maps of soil and yield parameters were produced using geographic information system and geostatistical methods. The strongest spatial correlation was found in the weight of 1000 grains and the weakest was in carbon flow. Temporal relationships were found between soil nitrate concentration, soil water content, and leaf area index. Wheat yield varied from 1.11 to 2.84 Mg ha(-1) and this remarkable variation indicates that the spatial analysis of soil and yield parameters is significant in organic agriculture.

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.

Interaction Effects of Light, Temperature and Nutrient Limitations (N, P and Si) on Growth, Stoichiometry and Photosynthetic Parameters of the Cold-Water Diatom Chaetoceros wighamii

Light (20-450 μmol photons m^-2 s^-1), temperature (3-11°C) and inorganic nutrient composition (nutrient replete and N, P and Si limitation) were manipulated to study their combined influence on growth, stoichiometry (C:N:P:Chl a) and primary production of the cold water diatom Chaetoceros wighamii. During exponential growth, the maximum growth rate (~0.8 d^-1) was observed at high temperture and light; at 3°C the growth rate was ~30% lower under similar light conditions. The interaction effect of light and temperature were clearly visible from growth and cellular stoichiometry. The average C:N:P molar ratio was 80:13:1 during exponential growth, but the range, due to different light acclimation, was widest at the lowest temperature, reaching very low C:P (~50) and N:P ratios (~8) at low light and temperature. The C:Chl a ratio had also a wider range at the lowest temperature during exponential growth, ranging 16-48 (weight ratio) at 3°C compared with 17-33 at 11°C. During exponential growth, there was no clear trend in the Chl a normalized, initial slope (α*) of the photosynthesis-irradiance (PE) curve, but the maximum photosynthetic production (P_m) was highest for cultures acclimated to the highest light and temperature. During the stationary growth phase, the stoichiometric relationship depended on the limiting nutrient, but with generally increasing C:N:P ratio. The average photosynthetic quotient (PQ) during exponential growth was 1.26 but decreased to <1 under nutrient and light limitation, probably due to photorespiration. The results clearly demonstrate that there are interaction effects between light, temperature and nutrient limitation, and the data suggests greater variability of key parameters at low temperature. Understanding these dynamics will be important for improving models of aquatic primary production and biogeochemical cycles in a warming climate.

Influence of light in the mixed-layer on the parameters of a three-component model of phytoplankton size class

Phytoplankton size structure is an important indicator of the state of the pelagic ecosystem. Stimulated by the paucity of in situ observations on size structure, and by the sampling advantages of autonomous remote platforms, new efforts are being made to infer the size-structure of the phytoplankton from oceanographic variables that may be measured at high temporal and spatial resolution, such as total chlorophyll concentration. Large-scale analysis of in situ data has revealed coherent relationships between size-fractionated chlorophyll and total chlorophyll that can be quantified using the three-component model of Brewin et al. (2010). However, there are variations surrounding these general relationships. In this paper, we first revise the three-component model using a global dataset of surface phytoplankton pigment measurements. Then, using estimates of the average irradiance in the mixed-layer, we investigate the influence of ambient light on the parameters of the three-component model. We observe significant relationships between model parameters and the average irradiance in the mixed-layer, consistent with ecological knowledge. These relationships are incorporated explicitly into the three-component model to illustrate variations in the relationship between size-structure and total chlorophyll, ensuing from variations in light availability. The new model may be used as a tool to investigate modifications in size-structure in the context of a changing climate.

Bacterial symbiosis in Syssitomya pourtalesiana Oliver, 2012 (Galeommatoidea: Montacutidae), a bivalve commensal with the deep-sea echinoid Pourtalesia.

For the first time, bacterial symbiosis is recognized in the bivalve family Montacutidae of the superfamily Galeommatoidea. The ctenidial filaments of Syssitomya pourtalesiana Oliver, 2012 are extended abfrontally and a dense layer of bacteriocyte cells cover the entire surface behind a narrow ciliated frontal zone. The bacteria are extracellular and held within a matrix of epithelial extensions and microvilli. There is no cuticular layer (glycocalyx) covering the bacteria as in many thyasirid symbioses. The bacteriocytes hold more than one morphotype of bacteria, but bacilli, 1–3 μm in length, dominate. Scanning electron microscopy observations show a surface mat of filamentous bacteria over the extreme abfrontal surfaces. Filter feeding was confirmed by the presence of food particles in the stomach and the bivalve is presumed to be mixotrophic. Syssitomya is commensal and lives attached to the anal spines of the deep-sea echinoid Pourtalesia. In this position, echinoid feeding currents and echinoid faecal material may supply the bacteria with a variety of nutrient materials including dissolved organic matter.

CoastColour Round Robin datasets: a database to evaluate the performance of algorithms for the retrieval of water quality parameters in coastal waters.

The use of in situ measurements is essential in the validation and evaluation of the algorithms that provide coastal water quality data products from ocean colour satellite remote sensing. Over the past decade, various types of ocean colour algorithms have been developed to deal with the optical complexity of coastal waters. Yet there is a lack of a comprehensive intercomparison due to the availability of quality checked in situ databases. The CoastColour Round Robin (CCRR) project, funded by the European Space Agency (ESA), was designed to bring together three reference data sets using these to test algorithms and to assess their accuracy for retrieving water quality parameters. This paper provides a detailed description of these reference data sets, which include the Medium Resolution Imaging Spectrometer (MERIS) level 2 match-ups, in situ reflectance measurements, and synthetic data generated by a radiative transfer model (HydroLight). These data sets, representing mainly coastal waters, are available from doi:10.1594/PANGAEA.841950. The data sets mainly consist of 6484 marine reflectance (either multispectral or hyperspectral) associated with various geometrical (sensor viewing and solar angles) and sky conditions and water constituents: total suspended matter (TSM) and chlorophyll a (CHL) concentrations, and the absorption of coloured dissolved organic matter (CDOM). Inherent optical properties are also provided in the simulated data sets (5000 simulations) and from 3054 match-up locations. The distributions of reflectance at selected MERIS bands and band ratios, CHL and TSM as a function of reflectance, from the three data sets are compared. Match-up and in situ sites where deviations occur are identified. The distributions of the three reflectance data sets are also compared to the simulated and in situ reflectances used previously by the International Ocean Colour Coordinating Group (IOCCG, 2006) for algorithm testing, showing a clear extension of the CCRR data which covers more turbid waters.

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.