We introduce the Global rRNA Universal Metabarcoding Plankton database (GRUMP), which consists of 1194 samples that were collected from 2003-2020 and cover extensive latitudinal and longitudinal transects, as well as depth profiles in all major ocean basins. DNA from unfractionated (> 0.2um) seawater samples was amplified using the 515Y/926R universal three-domain rRNA gene primers, simultaneously quantifying the relative abundance of amplicon sequencing variants (ASVs) from bacteria, archaea, eukaryotic nuclear 18S, and eukaryotic plastid 16S. Thus, the ratio between taxa in one sample is directly comparable to the ratio in any other GRUMP sample, regardless of gene copy number differences. This obviates a problem in prior global studies that used size-fractionation and different rRNA gene primers for bacteria, archaea, and eukaryotes, precluding comparisons across size fractions or domains. On average, bacteria contributed 71%, eukaryotes 19%, and archaea 8% to rRNA gene abundance, though eukaryotes contributed 32% at latitudes > 40. GRUMP is publicly available on the Simons Collaborative Marine Atlas Project (CMAP), promoting the global comparison of marine microbial dynamics.
Abstract. Nitrogen (N2) fixation, the energetically expensive conversion of N2 to ammonia, plays an important role in balancing the global nitrogen budget. Defying historic paradigms, recent studies have detected non-cyanobacterial N2 fixation in deep, dark oceanic waters. Even low volumetric rates can be significant considering the large volume of these waters. However, measuring aphotic N2 fixation is an analytical challenge due to the low particulate nitrogen (PN) concentrations. Here, we investigated N2 fixation rates in aphotic waters in the South China Sea (SCS). To increase the sensitivity of N2 fixation rate measurements, we applied a novel approach requiring only 0.28 μg N for measuring the isotopic composition of particulate nitrogen. We conducted parallel 15N2-enriched incubations in ambient seawater, seawater amended with amino acids and poisoned (HgCl2) controls, along with incubations that received no tracer additions to distinguish biological N2 fixation. Experimental treatments differed significantly from our two types of controls, those receiving no additions and killed controls. Amino acid additions masked N2 fixation signals due to the uptake of added 14N-amino acid. Results show that the maximum dark N2 fixation rates (1.28 ± 0.85 nmol N L−1 d−1) occurred within upper 200 m, while rates below 200 m were mostly lower than 0.1 nmol N L−1 d−1. Nevertheless, N2 fixation rates between 200 and 1000 m accounted for 39 ± 32 % of depth-integrated dark N2 fixation rates in the upper 1000 m, which is comparable to the areal nitrogen inputs via atmospheric deposition. Globally, we found that aphotic N2 fixation studies conducted in oxygenated environments yielded rates similar to those from the SCS (< 1 nmol N L−1 d−1), regardless of methods, while higher rates were occasionally observed in low-oxygen (< 62 µM) regions. Regression analysis suggests that particulate nitrogen concentrations could be a predictive proxy for detectable aphotic N2 fixation in the SCS and eastern tropical south Pacific. Our results provide the first insight into aphotic N2 fixation in SCS and support the importance of the aphotic zone as a globally-important source of new nitrogen to the ocean.
Abstract Heterotrophic bacteria and archaea (‘heteroprokaryotes’) drive global carbon cycling, but how to quantitatively organize their functional complexity remains unclear. We generated a global-scale understanding of marine heteroprokaryotic functional biogeography by synthesizing genetic sequencing data with a mechanistic marine ecosystem model. We incorporated heteroprokaryotic diversity into the trait-based model along two axes: substrate lability and growth strategy. Using genetic sequences along three ocean transects, we compiled 21 heteroprokaryotic guilds and estimated their degree of optimization for rapid growth (copiotrophy). Data and model consistency indicated that gradients in grazing and substrate lability predominantly set biogeographical patterns, and identified deep-ocean ‘slow copiotrophs’ whose ecological interactions control the surface accumulation of dissolved organic carbon.
Abstract Biological nitrogen fixation, the conversion of N2 gas into a more bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a research focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the abiotic factors that govern UCYN-A’s presence at the San Pedro Ocean Time-series (SPOT), its partner fidelity, and statistical interactions with non-symbiotic eukaryotes. 16S and 18S rRNA sequences were amplified by “universal primers” from monthly samples and resolved into Amplicon Sequence Variants, allowing us to observe multiple UCYN-A symbioses. UCYN-A1 relative abundances increased following the 2015-2016 El Niño event. When this “open ocean ecotype” was present, coastal upwelling ceased, and Ekman transport brought tropical waters into the region. Network analyses reveal all strains of UCYN-A co-occur with dinoflagellates including Lepidodinium , a potential predator, and parasitic Syndiniales . UCYN-A2 appeared to pair with multiple hosts and was not tightly coupled to its predominate host, while UCYN-A1 maintained a strong host-symbiont relationship. These biological relationships are particularly important to study in the context of climate change, which will alter UCYN-A distribution patterns both locally and globally.
Seasonal or chronic nutrient limitations in the photic zone limit large-scale cultivation of seaweed (macroalgae) in much of the world's oceans, hindering the development of macroalgae as a biofuel feedstock. One possible solution is to supply nutrients using a diel depth-cycling approach, physically moving the macroalgae between deep nutrient-rich water at night and shallow depths within the photic zone during the day. This study tested the effects of depth-cycling on the growth, morphology, and chemical composition of the giant kelp Macrocystis pyrifera, a target species for renewable biomass production. Giant kelp grown under depth-cycling conditions had an average growth rate of 5% per day and produced four times more biomass (wet weight) than individuals grown in a kelp bed without depth-cycling. Analysis of tissue from the depth-cycled kelp showed elevated levels of protein, lower C:N ratios, and distinct δ15N and δ13C values suggesting that the depth-cycled kelp were not nitrogen-deficient and assimilated nutrients from deep water. Depth-cycled kelp also exhibited smaller and thicker-walled pneumatocysts and larger blades. Overall, this study supports further investigation of depth-cycling as a macroalgal farming strategy.
Diazotrophic macroalgal associations (DMAs) can contribute fixed nitrogen (N) to the host macroalgae. Biological nitrogen fixation (BNF) rates investigated using acetylene reduction assays with living macroalgae surrounding Santa Catalina Island were low (maximum: 36 nmol N × g-1 (dw) × h-1 ) and probably insufficient towards helping meet macroalgal N demand. However, DMAs were observed during periods of low nitrate availability in Southern California coastal waters, highlighting the potential importance of diazotrophs during N depleted conditions. Eleven long-term (16-32 days) litter bag decomposition experiments with various macroalgae, especially those with high (> 10) C:N ratios, resulted in much higher BNF rates (maximum: 693 nmol N × g-1 (dw) × h-1 ) than observed with living macroalgae. BNF rates were lower at the beginning of macroalgal decomposition but rapidly increased during the second phase before declining towards the end of decomposition. Labile carbon availability is likely influencing BNF rates throughout macroalgal degradation and limits BNF in the final decomposition stage. Comparable dark and light BNF rates with most macroalgae surveyed suggest macroalgal detrital systems are an overlooked, potentially global, niche for heterotrophic N2 fixation. Lastly, suppressed BNF rates with sodium molybdate additions highlight the prevalence of sulfate reducing diazotrophs.
Macroalgae, commonly known as seaweed, are foundational species in coastal ecosystems and contribute significantly to coastal primary production globally. However, the impact of macroalgal decomposition on benthic biological nitrogen fixation (BNF) after deposition to the seafloor remains largely unexplored. In this study, we measure BNF rates at three different sites at the Big Fisherman's Cove on Santa Catalina Island, CA, USA, which is representative of globally distributed rocky bottom macroalgal habitats. Unamended BNF rates varied among sites (0.001–0.05 nmol N g −1 h −1 ) and were generally within the lower end of previously reported ranges. We hypothesized that the differences in BNF between sites were linked to the availability of organic matter. Indeed, additions of glucose, a labile carbon source, resulted in 2–3 orders of magnitude stimulation of BNF rates in bottle incubations of sediment from all sites. To assess the impact of complex, autochthonous organic matter, we simulated macroalgal deposition and remineralization with additions of brown (i.e., Macrocystis pyrifera and Dictyopteris ), green (i.e., Codium fragile ), and red (i.e., Asparagopsis taxiformis ) macroalgae. While brown and green macroalgal amendments resulted in 53- to 520-fold stimulation of BNF rates—comparable to the labile carbon addition—red alga was found to significantly inhibit BNF rates. Finally, we employed nifH sequencing to characterize the diazotrophic community associated with macroalgal decomposition. We observed a distinct community shift in potential diazotrophs from primarily Gammaproteobacteria in the early stages of remineralization to a community dominated by Deltaproteobacteria (e.g., sulfate reducers), Bacteroidia , and Spirochaeta toward the latter phase of decomposition of brown, green, and red macroalgae. Notably, the nifH -containing community associated with red macroalgal detritus was distinct from that of brown and green macroalgae. Our study suggests coastal benthic diazotrophs are limited by organic carbon and demonstrates a significant and phylum-specific effect of macroalgal loading on benthic microbial communities.
'%3e%3cpath fill='%23012169' d='M0 0v30h60V0z'/%3e%3cpath stroke='%23fff' stroke-width='6' d='m0 0 60 30m0-30L0 30'/%3e%3cpath stroke='%23C8102E' stroke-width='4' d='m0 0 60 30m0-30L0 30' clip-path='url(%23b)'/%3e%3cpath stroke='%23fff' stroke-width='10' d='M30 0v30M0 15h60'/%3e%3cpath stroke='%23C8102E' stroke-width='6' d='M30 0v30M0 15h60'/%3e%3c/g%3e%3c/svg%3e)
