Microbial eukaryotes are key components of the ocean plankton. Yet, our understanding of their community composition and activity in different water layers of the ocean is limited, particularly for ...picoeukaryotes (0.2-3 µm cell size). Here, we examined the picoeukaryotic communities inhabiting different vertical zones of the tropical and subtropical global ocean: surface, deep chlorophyll maximum, mesopelagic (including the deep scattering layer and oxygen minimum zones), and bathypelagic. Communities were analysed by high-tthroughput sequencing of the 18S rRNA gene (V4 region) as represented by DNA (community structure) and RNA (metabolism), followed by delineation of Operational Taxonomic Units (OTUs) at 99% similarity. We found a stratification of the picoeukaryotic communities along the water column, with assemblages corresponding to the sunlit and dark ocean. Specific taxonomic groups either increased (e.g., Chrysophyceae or Bicosoecida) or decreased (e.g., Dinoflagellata or MAST-3) in abundance with depth. We used the rRNA:rDNA ratio of each OTU as a proxy of metabolic activity. The highest relative activity was found in the mesopelagic layer for most taxonomic groups, and the lowest in the bathypelagic. Altogether, we characterize the change in community structure and metabolic activity of picoeukaryotes with depth in the global ocean, suggesting a hotspot of activity in the mesopelagic.
Summary
The main role of microorganisms in the cycling of the bulk dissolved organic carbon pool in the ocean is well established. Nevertheless, it remains unclear if particular bacteria ...preferentially utilize specific carbon compounds and whether such compounds have the potential to shape bacterial community composition. Enrichment experiments in the Mediterranean Sea, Baltic Sea and the North Sea (Skagerrak) showed that different low‐molecular‐weight organic compounds, with a proven importance for the growth of marine bacteria (e.g. amino acids, glucose, dimethylsulphoniopropionate, acetate or pyruvate), in most cases differentially stimulated bacterial growth. Denaturing gradient gel electrophoresis ‘fingerprints’ and 16S rRNA gene sequencing revealed that some bacterial phylotypes that became abundant were highly specific to enrichment with specific carbon compounds (e.g. Acinetobacter sp. B1‐A3 with acetate or Psychromonas sp. B3‐U1 with glucose). In contrast, other phylotypes increased in relative abundance in response to enrichment with several, or all, of the investigated carbon compounds (e.g. Neptuniibacter sp. M2‐A4 with acetate, pyruvate and dimethylsulphoniopropionate, and Thalassobacter sp. M3‐A3 with pyruvate and amino acids). Furthermore, different carbon compounds triggered the development of unique combinations of dominant phylotypes in several of the experiments. These results suggest that bacteria differ substantially in their abilities to utilize specific carbon compounds, with some bacteria being specialists and others having a more generalist strategy. Thus, changes in the supply or composition of the dissolved organic carbon pool can act as selective forces structuring bacterioplankton communities.
Aerobic anoxygenic phototrophic (AAP) bacteria are microorganisms that can harvest light energy using bacteriochlorophyll a to supplement their predominantly organotrophic metabolism. Growth ...enhancement by light has repeatedly been demonstrated in laboratory experiments with AAP isolates. However, the ecological advantage of light utilization is unclear, as it has never been proven in the natural environment. Here, we conducted manipulation experiments in the NW Mediterranean and found that AAP bacteria display high growth rates which are controlled to a large extent by intense grazing pressure and phosphorous availability. Foremost, we found that, contrarily to the bulk bacterioplakton, AAP bacteria display higher growth rates when incubated under light-dark cycles than in complete darkness. These results represent the first direct evidence that natural populations of marine AAP bacteria can be stimulated by light.
Incubation experiments with axenic cultures of four common phytoplankton species of the genera Chaetoceros, Skeletonema, Prorocentrum, and Micromonas were performed to test for the production of ...fluorescent dissolved organic matter (FDOM) by marine phytoplankton. Our results prove that the four species exuded both fluorescent protein-like and marine humic—like materials in variable amounts, with more production by the diatoms Chaetoceros sp. and Skeletonema costatum and less by Prorocentrum minimum. Whereas the exudation of protein-like substances by healthy phytoplankton cells has been recognized, the in sity production of marine humic-like substances is still a matter of debate. Using axenic cultures, we demonstrate unequivocally that phytoplankton can directly contribute to the autochthonous production of colored humic-like substances in the ocean. Extrapolation of these findings to the field indicates that about 20% of the marine humic—like substances produced in the highly productive coastal upwelling system of the Ría de Vigo could originate from growing phytoplankton. Therefore, the exudation of FDOM by marine phytoplankton should be considered in future studies of the dynamics of colored DOM in marine systems.
Ecosystem respiration is the biotic conversion of organic carbon to carbon dioxide by all of the organisms in an ecosystem, including both consumers and primary producers. Respiration exhibits an ...exponential temperature dependence at the subcellular and individual levels, but at the ecosystem level respiration can be modified by many variables including community abundance and biomass, which vary substantially among ecosystems. Despite its importance for predicting the responses of the biosphere to climate change, it is as yet unknown whether the temperature dependence of ecosystem respiration varies systematically between aquatic and terrestrial environments. Here we use the largest database of respiratory measurements yet compiled to show that the sensitivity of ecosystem respiration to seasonal changes in temperature is remarkably similar for diverse environments encompassing lakes, rivers, estuaries, the open ocean and forested and non-forested terrestrial ecosystems, with an average activation energy similar to that of the respiratory complex (approximately 0.65 electronvolts (eV)). By contrast, annual ecosystem respiration shows a substantially greater temperature dependence across aquatic (approximately 0.65 eV) versus terrestrial ecosystems (approximately 0.32 eV) that span broad geographic gradients in temperature. Using a model derived from metabolic theory, these findings can be reconciled by similarities in the biochemical kinetics of metabolism at the subcellular level, and fundamental differences in the importance of other variables besides temperature—such as primary productivity and allochthonous carbon inputs—on the structure of aquatic and terrestrial biota at the community level.
The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we ...analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H
oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) ...and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR‐amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR‐free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size‐fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular‐based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular‐based evaluations of entire phytoplankton communities.
see also the Perspective by Georgina L. Brennan
Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a ...coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality.
Abstract
Insights into the diversity of marine natural microbial biofilms, as for example those developing at the surface of marine macroalgae, can be obtained by using molecular techniques based on ...16S rRNA genes. We applied denaturing gradient gel electrophoresis (DGGE) with 16S rRNA genes–specific primers for Planctomycetes to compare the communities of these organisms developing on six different macroalgae (Chondrus crispus, Fucus spiralis, Mastocarpus stellatus, Porphyra dioica, Sargassum muticum, and Ulva sp.) sampled in spring 2012 in two rocky beaches in the north of Portugal. Planctomycetes can be one of the dominant organisms found in the epibacterial community of macroalgae, and we wanted to determine the degree of specificity and the spatial variation of these group. Shannon diversity indexes obtained from the comparison of DGGE profiles were similar in all the macroalgae, and in both sites, F. spiralis was the algae presenting lower Planctomycetes diversity, while M. stellatus and P. dioica from Porto showed the highest diversity. The analysis of DGGE profiles, including anosim statistics, indicate the existence of a specific Planctomycetes community associated with the algal host, likely independent of geographical variation. Sequencing of DGGE bands indicated that Planctomycetes communities were highly diverse, and some Operational Taxonomic Units seemed to be specifically associated with each macroalgae.
DGGE fingerprinting profile of the planctomycetes epiphytic communities in macroalgae and corresponding dendrogram evidencing the host-specificity of these communities.
Summary
Flow cytometry has revealed the existence of two distinct fractions of bacterioplankton cells, characterized by high and low nucleic acid contents (HNA and LNA cells). Although these ...fractions seem ubiquitous in aquatic systems, little is known concerning the variation in the cytometric parameters used to characterize them. We have performed cytometric analyses of samples from a wide range of aquatic systems to determine the magnitude and variability in the cytometric characteristics of HNA/LNA. We show that neither group is associated to a fixed level of fluorescence and of light scatter. Rather, the relative position of HNA and LNA in the fluorescence versus side scatter cytograms varies greatly, both within and among ecosystems. Although the cytometric parameters of both groups tend to covary, there is often uncoupling between the two, particularly in light scatter. Our results show that, although the basic HNA/LNA configuration is present in most samples, its cytometric expression changes greatly in different ecosystems and along productivity gradients. The patterns in cytometric parameters do not support the simple, dichotomous view of HNA and LNA as active and inactive cells, or the notion of two distinct and independent communities, but rather suggest that there may be cells that are intrinsic to each fraction, as well as others that may exchange between fractions.
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