Search

Coastal upwelling areas are extraordinarily productive environments where prokaryotic communities, the principal remineralizers of dissolved organic matter (DOM), rapidly respond to phytoplankton bloom and decay dynamics. Nevertheless, the extent of variability of key microbial functions in such dynamic waters remains largely unconstrained. Our metatranscriptomics analyses of 162 marker genes encoding ecologically relevant prokaryotic functions showed distinct spatial-temporal patterns in the NW Iberian Peninsula upwelling area. Short-term (daily) changes in specific bacterial functions associated with changes in biotic and abiotic factors were superimposed on seasonal variability. Taxonomic and functional specialization of prokaryotic communities, based mostly on different resource acquisition strategies, was observed. Our results uncovered the potential influence of prokaryotic functioning on phytoplankton bloom composition and development (e.g., Cellvibrionales and Flavobacteriales increased relative gene expression related to vitamin B12 and siderophore metabolisms during Chaetoceros and Dinophyceae summer blooms). Notably, bacterial adjustments to C- or N-limitation and DMSP availability during summer phytoplankton blooms and different spatial-temporal patterns of variability in the expression of genes with different phosphate affinity indicated a complex role of resource availability in structuring bacterial communities in this upwelling system. Also, a crucial role of Cellvibrionales in the degradation of DOM (carbohydrate metabolism, TCA cycle, proteorhodopsin, ammonium, and phosphate uptake genes) during the summer phytoplankton bloom was found. Overall, this dataset revealed an intertwined mosaic of microbial interactions and nutrient utilization patterns along a spatial-temporal gradient that needs to be considered if we aim to understand the biogeochemical processes in some of the most productive ecosystems in the world´s oceans.

Abstract Microbial heterotrophic activity is a major process regulating the flux of dissolved organic matter (DOM) in the ocean, while the characteristics of this DOM strongly influence its microbial utilization and fate in the ocean. In order to broaden the vertical resolution of leucine-to-carbon conversion factors (CFs), needed for converting substrate incorporation into biomass production by heterotrophic bacteria, 20 dilution experiments were performed in the North Atlantic Ocean. We found a depth-stratification in empirical CFs values from epipelagic to bathypelagic waters (4.00 ± 1.09 to 0.10 ± 0.00 kg C mol Leu−1). Our results demonstrated that the customarily used theoretical CF of 1.55 kg C mol Leu−1 in oceanic samples can lead to an underestimation of prokaryotic heterotrophic production in epi- and mesopelagic waters, while it can overestimate it in the bathypelagic ocean. Pearson correlations showed that CFs were related not only to hydrographic variables such as temperature, but also to specific phylogenetic groups and DOM quality and quantity indices. Furthermore, a multiple linear regression model predicting CFs from relatively simple hydrographic and optical spectroscopic measurements was attempted. Taken together, our results suggest that differences in CFs throughout the water column are significantly connected to DOM, and also reflect differences linked to specific prokaryotic groups.

Coastal ecosystems deteriorate globally due to human-induced stress factors, like nutrient loading and pollution. Bacteria are critical to marine ecosystems, e.g., by regulating nutrient cycles, synthesizing vitamins, or degrading pollutants, thereby providing essential ecosystem services ultimately affecting economic activities. Yet, until now bacteria are overlooked both as mediators and indicators of ecosystem health, mainly due to methodological limitations in assessing bacterial ecosystem functions. However, these limitations are largely overcome by the advances in molecular biology and bioinformatics methods for characterizing the genetics that underlie functional traits of key bacterial populations – “key” in providing important ecosystem services, being abundant, or by possessing high metabolic rates. It is therefore timely to analyze and define the functional responses of bacteria to human-induced effects on coastal ecosystem health. We posit that categorizing the responses of key marine bacterial populations to changes in environmental conditions through modern microbial oceanography methods will allow establishing the nascent field of genetic counselling for our coastal waters. This requires systematic field studies of linkages between functional traits of key bacterial populations and their ecosystem functions in coastal seas, complemented with systematic experimental analyses of the responses to different stressors. Research and training in environmental management along with dissemination of results and dialogue with societal actors are equally important to ensure the role of bacteria is understood as fundamentally important for coastal ecosystems. Using the responses of microorganisms as a tool to develop genetic counselling for coastal ecosystems can ultimately allow for integrating bacteria as indicators of environmental change.

Marine microorganisms are involved in a variety of biogeochemical cycles and live in diverse ecological communities where they interact with each other and with other organisms to guarantee ecosystem functions. The present study focused on a shallow marine environment located in Ría de Vigo (NW, Spain), where sediment and size-fractionated plankton samples were collected from 2016 to 2018. DNA metabarcoding was used to describe the eukaryote and prokaryote composition and diversity in sediments and plankton and to depict possible associations among the most frequent and abundant organisms by co-occurrence network analysis. High eukaryote and prokaryote diversity indices were obtained in all compartments. Significant differences among eukaryote and prokaryote communities were found between sediment and plankton samples, with a high percentage of exclusive operational taxonomic units (OTUs) associated with each compartment, especially from sediment. Despite these differences, shared taxa between water and sediment were also obtained, suggesting a relatively meaningful exchange of organisms between both environmental compartments. Significant co-occurrences were mainly obtained between prokaryotes (41%), followed by eukaryotes–prokaryotes (32%) and between eukaryotes (27%). The abundant and strong positive correlations between organisms, including representatives from the sediment and the water column, suggested an essential role of biotic interactions as community-structuring factors in shallow waters where beneficial associations likely prevail. This study provides a novel approach for the detailed description of the eukaryote and prokaryote diversity and co-occurrence patterns in a shallow marine area, including both the sediment and different water-size fractions. The high diversity obtained and the detection of predominantly coexisting interactions among organisms from sediment and the overlying water column suggest a movement of species between both habitats and therefore confirm the importance of integratively studying shallow marine ecosystems.

Knowledge of the magnitude and variability of plankton respiration is a crucial gap in our understanding of marine carbon cycling. In order to validate the INT reduction method as a proxy for plankton respiration, we have compiled and analyzed a dataset (n = 376) of concurrent measurements of dissolved oxygen consumption (CRO2) and in vivo reduction of 2-para (iodophenyl)-3(nitrophenyl)-5(phenyl) tetrazolium chloride tetrazolium salt (INT) spanning a wide range of oceanic regions and physicochemical conditions. Data were randomly divided into two independent subgroups: two thirds of the data were used to derive a regression conversion between dissolved oxygen consumption and INT reduction (“training” dataset) and one third of the data was used to validate the regression (“test” dataset). There was a significant relationship between the log-transformed dissolved oxygen consumption rates and the log-transformed INT reduction rates (INTT) with the “training” dataset (logCRO2 = 0.72logINTT + 0.44, R2 = 0.69, n = 249, p < 0.001). The estimated oxygen consumption rates obtained applying the former equation were compared to the measured dissolved oxygen consumption rates from the “test” dataset which spans over three orders of magnitude range of respiration rates. There was no significant difference between the measured and estimated dissolved oxygen consumption rates, indicating that the INT reduction method can be used as a proxy for respiration in natural plankton communities. Further analysis dividing the data by temperature and chlorophyll-a concentration, indicated that the predictive capacity of the empirical conversion equation is increased at temperatures >8°C and chlorophyll-a concentrations >0.2 μg L-1 and reduced at lower temperatures and chlorophyll-a concentrations. The results of this study endorse the adequate performance and reliability of the INT method for natural plankton communities.

Bacterial abundance, biomass and heterotrophic activity, along with hydrographic and phytoplankton variables, were measured from February 1998 to September 1999 at two coastal stations off A Coruña (Galicia, NW Spain). Bacterial abundance varied from 0.1 to 1.8 x 106 cells ml-1 and water-column integrated bacterial production ranged from 34 to 1132 mg C m-2 d-1. Two annual maxima of bacterial abundance and production were observed, in spring and summer, although relatively high abundance values remained until autumn. In autumn and winter production values were low with the exception of the results obtained in November 1998, when the highest values of bacterial production of the whole study were observed at both stations. Bacterial biomass constituted a significant, but low, fraction of particulate organic carbon (4-21 %) and was always lower than phytoplankton biomass (up to 40% of phytoplankton carbon). Also, bacterial production was generally < 30% of primary production, but in some situations (as in early spring or in autumn) bacterial production exceeded primary production, suggesting a delayed response of bacterial activity after a phytoplankton bloom.