11 research outputs found
Assessment of microbial plankton diversity as an ecological indicator in the NW Mediterranean coast
High-throughput sequencing of microbial assemblages has been proposed as an alternative methodology to the traditional ones used in marine monitoring and environmental assessment. Here, we evaluated pico- and nanoplankton diversity as ecological indicators in NW Mediterranean coastal waters by comparing their diversity in samples subjected to varying degrees of continental pressures. Using metabarcoding of the 16S and 18S rRNA genes, we explored whether alphadiversity indices, abundance of Operational Taxonomic Units and taxonomic groups (and their ratios) provide information on the ecological quality of coastal waters. Our results revealed that only eukaryotic diversity metrics and a limited number of prokaryotic and eukaryotic taxa displayed potential in assessing continental influences in our surveyed area, resulting thus in a restrained potential of microbial plankton diversity as an ecological indicator. Therefore, incorporating microbial plankton diversity in environmental assessment could not always result in a significant improvement of current marine monitoring strategies.Preprint2,35
Seasonality of biogeohemically relevant genes in the NW Mediterranean coastal microbiome
Marine biogeochemical processes are mediated by microorganisms through protein
encoding genes, some being solely present in prokaryotes. During the last decade,
genomic site-specific and large-scale expeditions have discovered millions of genes,
unveiling new putative functions and large gene phylogenetic heterogeneity.
Nonetheless, little still is known about the genomic basis of key biogeochemical
processes, the taxonomic groups mediating them and whether seasonal patterns occur
across taxonomic levels. For these reasons, we conducted temporal analyses of the
functional diversity for 18 key functional genes in a model coastal marine microbiome.
We analyzed a 3-year metagenomic time-series from the Blanes Bay Microbial
Observatory (NW Mediterranean Sea) through state-of-the-art omics’ tools and time
series statistics. Using a new Protein-Level ASSembler (PLASS), based in assembling at
the protein space, a large number of potentially new and potentially biogeochemically
relevant genes were recovered, which were missed by standard metagenomic analyses.
This allowed us to explore the seasonal trends and gene heterogeneity in various key
genes involved in the four major marine biogeochemical cycles (carbon, phosphorus,
sulfur and nitrogen). Preliminary results show some key functions as seasonal, although
with heterogeneity across the different taxonomical ranks. Our results define the
seasonality of gene presence in that coastal environment and are the basis to discuss
the implications of the seasonality of such genes for ecosystem functionin
Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing
High-throughput sequencing (HTS) of the 16S rRNA gene has been
used successfully to describe the structure and dynamics of microbial communities.
Picocyanobacteria are important members of bacterioplankton communities, and,
so far, they have predominantly been targeted using universal bacterial primers,
providing a limited resolution of the picocyanobacterial community structure
and dynamics. To increase such resolution, the study of a particular target group
is best approached with the use of specific primers. Here, we aimed to design
and evaluate specific primers for aquatic picocyanobacterial genera to be used
with high-throughput sequencing. Since the various regions of the 16S rRNA
gene have different degrees of conservation in different bacterial groups, we
therefore first determined which hypervariable region of the 16S rRNA gene provides the highest taxonomic and phylogenetic resolution for the genera Synechococcus, Prochlorococcus, and Cyanobium. An in silico analysis showed that
the V5, V6, and V7 hypervariable regions appear to be the most informative for
this group. We then designed primers flanking these hypervariable regions and
tested them in natural marine and freshwater communities. We successfully detected that most (97%) of the obtained reads could be assigned to picocyanobacterial genera. We defined operational taxonomic units as exact sequence variants (zero-radius operational taxonomic units [zOTUs]), which allowed us to detect
higher genetic diversity and infer ecologically relevant information about picocyanobacterial community composition and dynamics in different aquatic systems. Our results open the door to future studies investigating picocyanobacterial diversity in
aquatic systems
Quantifying long-term recurrence in planktonic microbial eukaryotes
How much temporal recurrence is present in microbial assemblages is still an unanswered ecological question. Even though marked seasonal changes have been reported for whole microbial communities, less is known on the dynamics and seasonality of individual taxa. Here, we aim at understanding microbial recurrence at three different levels: community, taxonomic group and operational taxonomic units (OTUs). For that, we focused on a model microbial eukaryotic community populating a long-term marine microbial observatory using 18S rRNA gene data from two organismal size fractions: the picoplankton (0.2–3 µm) and the nanoplankton (3–20 µm). We have developed an index to quantify recurrence in particular taxa. We found that community structure oscillated systematically between two main configurations corresponding to winter and summer over the 10 years studied. A few taxonomic groups such as Mamiellophyceae or MALV-III presented clear recurrence (i.e., seasonality), whereas 13%–19% of the OTUs in both size fractions, accounting for ~40% of the relative abundance, featured recurrent dynamics. Altogether, our work links long-term whole community dynamics with that of individual OTUs and taxonomic groups, indicating that recurrent and non-recurrent changes characterize the dynamics of microbial assemblages
Factors controlling the community structure of picoplankton in contrasting marine environments.
The effect of inorganic nutrients on planktonic assemblages has traditionally relied on concentrations rather
than estimates of nutrient supply. We combined a novel
dataset of hydrographic properties, turbulent mixing, nutrient concentration, and picoplankton community composition
with the aims of (i) quantifying the role of temperature, light,
and nitrate fluxes as factors controlling the distribution of autotrophic and heterotrophic picoplankton subgroups, as determined by flow cytometry, and (ii) describing the ecological niches of the various components of the picoplankton
community. Data were collected at 97 stations in the Atlantic
Ocean, including tropical and subtropical open-ocean waters,
the northwestern Mediterranean Sea, and the Galician coastal
upwelling system of the northwest Iberian Peninsula. A generalized additive model (GAM) approach was used to predict depth-integrated biomass of each picoplankton subgroup
based on three niche predictors: sea surface temperature, averaged daily surface irradiance, and the transport of nitrate
into the euphotic zone, through both diffusion and advection. In addition, niche overlap among different picoplankton
subgroups was computed using nonparametric kernel density functions. Temperature and nitrate supply were more
relevant than light in predicting the biomass of most picoplankton subgroups, except for Prochlorococcus and lownucleic-acid (LNA) prokaryotes, for which irradiance also
played a significant role. Nitrate supply was the only factor that allowed the distinction among the ecological niches
of all autotrophic and heterotrophic picoplankton subgroups.
Prochlorococcus and LNA prokaryotes were more abundant
in warmer waters ( > 20 ◦C) where the nitrate fluxes were
low, whereas Synechococcus and high-nucleic-acid (HNA)
prokaryotes prevailed mainly in cooler environments characterized by intermediate or high levels of nitrate supply. Finally, the niche of picoeukaryotes was defined by low temperatures and high nitrate supply. These results support the
key role of nitrate supply, as it not only promotes the growth
of large phytoplankton, but it also controls the structure of
marine picoplankton communitie
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities
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 H2 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.En prensa10,01