Global diversity and biogeography of deep-sea pelagic prokaryotes

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Empirical leucine-to-carbon conversion factors for estimating heterothrophic bacterial production in surface waters of the world oceans

Comunicación oralBacterial biomass production is a key parameter for evaluating the role of bacterioplankton in ocean carbon cycling. However, bacterial production cannot be directly measured and is typically estimated from the incorporation rates of radiolabelled leucine. The conversion of leucine uptake rates into bacterial carbon production rates requires the use of conversion factors (CFs) which must be empirically determined. Despite the empirical leucine-to-carbon CFs vary widely across environments very little is known about its potential controlling factors. We conducted a set of 10 surface seawater cultures experiments where the growth of the natural bacterial assemblage was promoted by filtration (removal of grazers) or by both filtration and dilution. Sampling stations were located between 30 ºN and 30 ºS, including the Atlantic, Pacific and Indian oceans. CFs varied from 0.13 to 1.47 Kg C mol Leu-1, being higher in the filtrated than in the filtrated and diluted treatment. The abundance of picocyanobacteria explained 60% of the observed variability. Our results further suggest that the composition of bacterioplankton, as assessed by ARISA fingerprinting, may partially explain the observed variation in CFs

Sample dilution and bacterial community composition influence empirical leucine-to-carbon conversion factors in surface waters of the world's oceans

Research articleThe transformation of leucine incorporation into prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world’s oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e. removal of grazers; F treatment) or filtration combined with dilution (i.e. relieving also resource competition; FD treatment). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu-1 and were significantly lower in the filtered and diluted (FD) than in the filtered (F) treatments. Also, changes in bacterial community composition during the incubations, as assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA), were stronger in the FD than in the F treatments, as compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCFs determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus) and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCFs variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts although resulting into relatively low carbon production rates in the oligotrophic ocean.En prensa3,829

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems

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

Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2_2 fixation

Marine diazotrophs convert dinitrogen (N2) gas into bioavailable nitrogen (N), supporting life in the global ocean. In 2012, the first version of the global oceanic diazotroph database (version 1) was published. Here, we present an updated version of the database (version 2), significantly increasing the number of in situ diazotrophic measurements from 13 565 to 55 286. Data points for N2 fixation rates, diazotrophic cell abundance, and nifH gene copy abundance have increased by 184 %, 86 %, and 809 %, respectively. Version 2 includes two new data sheets for the nifH gene copy abundance of non-cyanobacterial diazotrophs and cell-specific N2 fixation rates. The measurements of N2 fixation rates approximately follow a log-normal distribution in both version 1 and version 2. However, version 2 considerably extends both the left and right tails of the distribution. Consequently, when estimating global oceanic N2 fixation rates using the geometric means of different ocean basins, version 1 and version 2 yield similar rates (43–57 versus 45–63 Tg N yr−1; ranges based on one geometric standard error). In contrast, when using arithmetic means, version 2 suggests a significantly higher rate of 223±30 Tg N yr−1 (mean ± standard error; same hereafter) compared to version 1 (74±7 Tg N yr−1). Specifically, substantial rate increases are estimated for the South Pacific Ocean (88±23 versus 20±2 Tg N yr−1), primarily driven by measurements in the southwestern subtropics, and for the North Atlantic Ocean (40±9 versus 10±2 Tg N yr−1). Moreover, version 2 estimates the N2 fixation rate in the Indian Ocean to be 35±14 Tg N yr−1, which could not be estimated using version 1 due to limited data availability. Furthermore, a comparison of N2 fixation rates obtained through different measurement methods at the same months, locations, and depths reveals that the conventional 15N2 bubble method yields lower rates in 69 % cases compared to the new 15N2 dissolution method. This updated version of the database can facilitate future studies in marine ecology and biogeochemistry. The database is stored at the Figshare repository (https://doi.org/10.6084/m9.figshare.21677687; Shao et al., 2022)