A range of new techniques have allowed for unprecedented insight into the biodiversity and functioning of marine microbiomes. These approaches are revealing the complex linkages between genotype evolution, gene expression, microbiome interactions, and large-scale biogeochemical cycles. In this session, we encourage submissions focused on lab and/or field measurements of how microbiomes interact with their environment, new approaches for understanding microbiome diversity-functioning relationships, and novel applications of models and theory for how microbial physiology and biodiversity control key ecosystem functions or biogeochemical cycles. We hope to bring together a wide range of researchers interested in ocean microbial diversity and functioning.
Lead Organizer: Adam Martiny, University of California, Irvine (amartiny@uci.edu)
Co-organizers:
Luke Thompson, NOAA Atlantic Oceanographic and Meteorological Laboratory (luke.thompson@noaa.gov)
Presentations
06:30 PM
NITROGEN FIXATION RATES INCREASE WITH DIAZOTROPH RICHNESS IN THE GLOBAL OCEAN (7431)
Primary Presenter: Dominic Eriksson, ETHZ (deriksson@ethz.ch)
Marine diazotrophs convert atmospheric nitrogen gas into bioavailable nitrogen that can fuel up to 50% of the primary productivity in oligotrophic subtropical and tropical seas. Despite their importance, little is known about their global biogeography and diversity since global studies have been hampered by scarce data observations within the marine environment. This limitation prevents us from understanding the link between diazotroph richness and ecosystem function, especially nitrogen fixation as this is the main bioavailable nitrogen source in oligotrophic oceans. To analyse the correlation between global richness and nitrogen fixation rates, we integrate -omics and traditional microscopic based observations and make use of Species Distribution Models that have been developed to cope with datasets that suffer from uneven sampling efforts and scarce observations. Global diazotroph richness is generally high in subtropical and tropical marine regions declining polewards. Our results show that sea surface temperature (mean adjusted R2 of 0.17) and nutrient-related environmental parameters (mean adjusted R2 of 0.11 - 0.14) rank as the most important predictors on a global scale and biogeographic pattern strongly overlap in tropical regions supporting concepts such as niche complementarity. Additionally, we provide the first global biogeographic pattern of non-cyanobacterial diazotrophs that show increased probability of occurrences within upwelling regions when contrasted to cyanobacterial diazotrophs. This result further links to the hypothesized niche of non cyanobacterial diazotrophs to be found in nutrient rich waters containing higher concentrations of particulate organic carbon, where oxygen poor microniches provide a sheltered environment for the oxygen sensitive nitrogenase enzyme. Finally, to assess the relationship between global diazotroph richness and ecosystem function, we analysed the correlation between our global richness projections and global nitrogen fixation rates from two separate publications and found a positive relationship between global diazotroph richness and nitrogen fixation rates (R = 0.74, p < 0.001; R = 0.66, p < 0.001) supporting the resource use efficiency hypothesis.
06:30 PM
METABOLIC INTERACTOMES UNVEIL FUNCTIONAL SEASONALITY IN A TIME SERIES ANALYSIS (4986)
Primary Presenter: Nestor Arandia Gorostidi, Institut de Ciències del Mar (ICM-CSIC) (arandia@icm.csic.es)
Ecological network analysis has become a particularly useful tool for studying microbial associations in marine environments. Using taxonomic information (typically using the small subunit ribosomal gene as a marker), ecological network analysis has resolved the co-occurrence between different taxonomic units (or species), disclosing potential biotic (microbe-microbe) interactions. However, the study of taxonomical associations alone cannot reveal the metabolic and functional rationale of such interactions. In the current work, we combine metagenomic data of a Mediterranean time-series dataset for picoeukaryotic and prokaryotic cells and ecological network analysis to analyze the associations between key genes involved in different metabolic pathways. We observe abundant potential interactions at the gene level, suggesting widespread metabolic associations between marine microbes. Metabolism of vitamins (including de novo synthesis of cobalamin) shows the highest degree of correlations with other metabolic functions, highlighting vitamins as a key component shaping microbial community structure. Other genes related to nitrogen metabolisms, such as amoA and nitrite reductase (nirK) genes, and genes involved in urea production through purine degradation, also show a strong correlation between them in winter, indicating that during this season microbes may interact between them through nitrogen metabolism. Our preliminary results reveal that gene-based networks are an especially powerful tool to analyze possible metabolic interactions and may facilitate the proposition and future testing of such interaction hypotheses.
06:30 PM
DEEP LEARNING GATEWAYS TO ILLUMINATING THE FUNCTIONAL POTENTIAL AND ECOSYSTEM FUNCTION OF ‘MICROBIAL DARK MATTER’ (6952)
Primary Presenter: Adrienne Hoarfrost, University of Georgia (adrienne.l.hoarfrost@gmail.com)
A staggering majority of microbial sequences from the marine environment can’t be functionally annotated with standard bioinformatic approaches. This “microbial dark matter” is typically ignored in downstream analysis, introducing a severe bias at the very first preprocessing step. Deep learning approaches, in contrast, can learn useful representations of sequences based on the sequence context itself, for every sequence, without reference to external databases or need for metagenomic assembly. We are using deep learning approaches to link all microbial information from environmental metagenomes to the functional potential and ecosystem function of microbiomes, and developing strategies to overcome the high-dimensionality, low-sample-size problem inherent to biology. We will present LookingGlass, a deep learning foundation model embedding functional information for read-length prokaryotic DNA sequences. LookingGlass predicts functional annotation for all reads with 82% accuracy to the 4th EC number. Applying LookingGlass to account for the full functional diversity of marine metagenomes, we observe fundamentally different geospatial patterns in functional diversity across latitude and depth than those achieved with standard bioinformatic approaches, suggesting that accounting for “microbial dark matter” is fundamental to our ability to link microbiomes to ecosystem function. Going forward, we are using LookingGlass as a stepstone to model the relationships between microbial community members to predict complex community-level phenotypes that drive the marine carbon cycle.
06:30 PM
DIAZOTROPH COMMUNITY AND ACTIVITY IN THE SOUTHERN INDIAN OCEAN (4797)
Primary Presenter: Subhadeep Chowdhury, Mediterranean Institute of Oceanography, Aix Marseille University (subhadeep.chowdhury@mio.osupytheas.fr)
Dinitrogen (N2) fixers (diazotrophs) drive primary productivity by supplying reactive nitrogen to marine ecosystems and promoting CO2 uptake. N2 fixation is considerably well-known and explored in the low latitudes of the Atlantic and Pacific Oceans. The Indian Ocean, however, remains a widely under-sampled region and an overlooked contributor to the global nitrogen budget. Here, we investigated N2 fixation activity, diazotroph community composition, and diazotroph abundance across the multi-frontal system that separates the oligotrophic waters of the south Indian Ocean gyre from the HNLC waters of the Southern Ocean in the context of the nutrient and trace metal environment. We find a sharp contrast in the distribution of diazotroph groups across the frontal system, with cyanobacterial diazotrophs preferring warm oligotrophic waters in the gyre and non-cyanobacterial diazotrophs being more abundant in the cold nutrient-rich waters of the southern ocean. Our results show a well-defined succession of diazotroph communities associated with the southern Indian Ocean fronts. These findings expand the range of biomes in which diazotrophy can be observed, and provide new insights into diazotrophy in an understudied region.
06:30 PM
Single-cell genomics reveals the genome content of the uncultured cyanobacterial diazotroph UCYN-A3 (5185)
Primary Presenter: Cinthya Vieyra, Institute of Marine Sciences - CSIC (cvieyra@icm.csic.es)
The unicellular cyanobacteria Candidatus Atelocyanobacterium thalassa (hereafter, UCYN-A) are important nitrogen fixers that live in symbiosis with the haptophyte algae Braarudosphaera bigelowii and its close relative species. Although the UCYN-A phylogenetic group includes at least six sublineages, only the genomes of UCYN-A1 and UCYN-A2 had been sequenced to date. Therefore, despite its biogeochemical relevance, comparative genomics on the UCYN-A phylogenetic group has been limited by the poor representation of genomic data. Here, using a high-throughput DNA sequencing approach on a single sorted cell from the South Atlantic Ocean, we reconstructed about 65% of the genome of the UCYN-A3 sublineage. We show that although the genomic content of UCYN-A3 is very similar to the previously sequenced UCYN-A1 and UCYN-A2 sublineages, there are some differential genomic features such as the presence of genes for cell shape and cell wall biogenesis, as well as genes implicated in pyrimidine metabolism that are only present in UCYN-A2 and UCYN-A3. Also, comparative genomics suggests that the three sublineages form a monophyletic group that diverged from a common ancestor with a reduced genome, with UCYN-A2 being the closest to UCYN-A3 and UCYN-A1 its relative. Finally, phylogenomic and molecular clock analyses were also performed to estimate the age of divergence of the UCYN-A1, UCYN-A2 and UCYN-A3 sublineages both within the UCYN-A group and in a broader phylogenetic context, thus providing a paleo-oceanographic context for when these UCYN-A sublineages originated.
06:30 PM
Bacterial community dynamics and predictive function of surf zone seawater in a recreational beach in Ostend, Belgium (5236)
Primary Presenter: Yunmeng Li, Flanders Marine Institute (yunmeng.li@vliz.be)
Coastal seawater hosts diverse bacteria that perform various functions, such as decomposing organic matter, nitrogen cycling, and serving as food for other organisms. In addition to the ecological importance, bacteria present in seawater can also affect human health if they are inhaled, ingested or get in contact with skin. Understanding the bacterial community in coastal seawater is therefore essential for both ecological and public health reasons. The surf zone, where sea spray aerosols are formed, is of particular interest due to the potential for increased bacterial concentrations and interactions with beachgoers. This study aimed to investigate the bacterial community and their function in the surf zone. We collected 72 surface seawater samples from a recreational beach in Ostend, Belgium from March 2018 to November 2019. Bacterial communities were analyzed using full-length 16S rDNA nanopore sequencing. Potential bacterial functions were determined using the FAPROTAX database. Biotic and abiotic factors, obtained from the “Ocean Productivity” and “Meetnet Vlaamse Banken” databases, were examined as the drivers of bacterial community and function using the Mantel test. The results showed that spring seawater had a higher number of unique taxa at the family level. The relative abundance of Rhodobacteraceae and dark sulfur oxidation function were higher in spring seawater, mostly driven by Chl a, indicating a higher potential for the formation of dimethylsulphide (DMS) and therefore the formation of secondary marine aerosols and cloud condensation nuclei.
06:30 PM
Iron physiology and metabolism of phytoplankton in a continental shelf ecosystem (6204)
Primary Presenter: Lucy Quirk, University of Georgia (lucye.quirk@gmail.com)
Continental shelf ecosystems host diverse phytoplankton communities responsible for large portions of global primary productivity. The South Atlantic Bight (SAB) is a continental shelf transition zone extending from the Southeastern US coast to the Sargasso Sea. Iron availability is hypothesized to decrease with distance from shore, reflecting an iron gradient along the SAB. Phytoplankton communities across the shelf therefore may engage in distinct metabolic strategies as a function of iron status. To examine this, we grew inner and outer shelf diatom (Cylindrotheca) and coccolithophore (Gephyrocapsa oceanica and Emiliania huxleyi respectively) isolates under high and low iron conditions. The inner shelf diatom displayed the highest growth rates, reflecting this group’s bloom-forming capabilities in dynamic environments. E. huxleyi sustained 75% of its maximum growth rate in the low iron treatment, supporting that certain coccolithophores may be well adapted to low iron conditions on the outer continental shelf. Hybrid transcriptomes are being assembled using Illumina NextSeq short reads (~150 base pairs, 112 million reads) and Pacific Biosciences HiFi long reads (~1600 base pairs, 6 million reads). Comparing physiology metrics and gene expression across isolates and among shelf regions will aid in our understanding of phytoplankton ecology in transitional continental shelf ecosystems.
06:30 PM
Polyphosphate in marine heterotrophic bacteria as an energy storage (6489)
Primary Presenter: Rixuan GAO, Hong Kong University of Science and Technology (HKUST) (rgaoah@connect.ust.hk)
Marine heterotrophic bacteria rely on exogenous organic compounds for their survival and growth. The supply of dissolved organic carbon (DOC) from autotrophs, on the other hand, is controlled by the availability of productivity limiting nutrients, e.g., nitrogen and phosphorus (P). The balance/competition between carbon (C) and nutrient limitations can potentially affect the ecological functions of marine microbial communities. In this talk, we explore the possibility of an intracellular compound, polyphosphate (polyP), in regulating this balance. PolyP is a polymer of phosphate residues linked by high-energy phosphoanhydride bonds, known to be an energy and/or P source for polyP-accumulating organisms. We hypothesize that marine heterotrophic bacteria can cope with the limitation of DOC using dynamic metabolisms of polyP. Using laboratory experiments of pure bacterial culture and natural seawater communities, we show that DOC and inorganic phosphate supply can affect cellular polyP dynamics. PolyP is an energy storage for marine heterotrophic bacteria during C limitation rather than P storage, and the release of phosphate from polyP degradation can support ambient autotrophy.
06:30 PM
THE NEREA AUGMENTED OBSERVATORY IN THE GULF OF NAPLES (ITALY): A HOLISTIC APPROACH TO ECOLOGICAL LONG-TERM RESEARCH (6611)
Primary Presenter: Raffaella Casotti, Stazione Zoologica Anton Dohrn (raffa@szn.it)
In the last decades, multidisciplinary studies combining classical methods, to investigate the marine environment and its biological communities, with multiple omics approaches (metagenomics, metatranscriptomics, proteomics, metabolomics) have been implemented. The challenge of these studies is to address questions concerning the functional role of its components with a holistic approach. We present here the rationale and potential of the NEREA (Naples Ecological REsearch for Augmented observatories) Observatory, aimed at including biomolecular parameters into standard oceanographic observations at three main sites of the Gulf of Naples. Traditional physical, chemical, and biological measurements integrate metabarcoding, metagenomics, metatranscriptomics on several size fractions, so to have a better representation of plankton taxonomical but also functional diversity. Three sites are regularly visited at different pace (monthly, seasonally, biannualy), to better represent coastal, river-influenced and offshore deep areas of the Gulf. Based on the legacy of the Long Term Ecological research (LTER) site MareChiara in one of the sites, the ambition of NEREA is to represent a playground for plankton (but not only) process studies, based on the long-term knowledge of plankton dynamics acquired in more than 30 years of observations. The NEREA dataset will become available shortly after acquisition following the FAIR principles and will be made available to the scientific community for comparative and collaborative research.
06:30 PM
Isolation and ecophysiology of a novel Roseobacter CHAB-I-5 isolate, US3C007 (7230)
Primary Presenter: V. Celeste Lanclos, University of Southern California (lanclos@usc.edu)
The Roseobacter CHAB-I-5 cluster makes up to 20% of Roseobacters and 6% of bacterioplankton cells in surface oceans. Their genomes provide evidence of genome streamlining and the metabolic potential for aerobic anoxygenic photosynthesis (AAnP). Physiological tests of these processes has not previously been possible due to the inability to reliably propagate live cultures. We have isolated a new CHAB-I-5 representative, US3C007, from surface waters at the San Pedro Ocean Time Series (SPOT) through dilution-to-extinction cultivation techniques in artificial seawater media. Preliminary 16S rRNA gene identification using NCBI BLAST resulted in a 100% match to the previously published isolate, SB2, that was lost. We sequenced US3C007’s genome using a combination of long and short reads and assembled using Flye, which resulted in a complete circular genome at 3,622,411 bp. US3C007 and SB2 share 98.68% average nucleotide identity to each other, making US3C007 an ideal candidate to understand CHAB-I-5 physiology. Scanning electron microscopy shows pleiomorphy in the axenic culture with most cells exhibiting coccobacillus shape in doublets or lines of quadruplets. Salinity tolerance experiments showed growth at salinities between 28-40.5, with an optimum salinity of 33.7 at an average of 0.72 doublings/day. Temperature tolerance experiments showed growth between 16˚C-26˚C. Preliminary genomic analysis indicates the presence of genes for AAnP in our isolate, and ongoing work is focused on verifying AAnP, single nitrogen source utilization, and carbon requirements for US3C007.
SS063P Linking Ocean Microbiomes and Ecosystem Functions
Description
Time: 6:30 PM
Date: 7/6/2023
Room: Mezzanine