The importance of zinc (Zn) as a nutrient and its ability to be substituted for by cobalt (Co) have been characterized in model marine diatoms. However, the extent to which this substitution ...capability is distributed among diatom taxa is unknown. Zn/Co metabolic substitution was assayed in four diatom species as measured by the effect of free ion concentrations of Zn2+ and Co2+ on specific growth rate. Analysis of growth responses found substitution of these metals can occur within the northwest Atlantic isolate Thalassiosira pseudonana CCMP1335, the northeast Atlantic isolate Phaeodactylum tricornutum CCMP632, and within the northeast Pacific isolates Pseudo-nitzschia delicatissima UNC1205 and Thalassiosira sp. UNC1203. Metabolic substitution of Co in place of Zn in the Atlantic diatoms supports their growth in media lacking added Zn, but at the cost of reduced growth rates. In contrast, highly efficient Zn/Co substitution that supported growth even in media lacking added Zn was observed in the northeast Pacific diatoms. We also present new data from the northeast Pacific Line P transect that revealed dissolved Co and Zn ratios (dCo : dZn) as high as 3.52 : 1 at surface (0–100 m) depths. We posit that the enhanced ability of the NE Pacific diatoms to grow using Co is an adaptation to these high surface dCo : dZn ratios. Particulate metal data and single-cell metal quotas also suggest a high Zn demand in diatoms that may be partially compensated for by Co.
Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a ...5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO
, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.
Dinitrogen (N2) fixation is recognized as an important input of new nitrogen (N) to the open ocean gyres, contributing to the export of organic matter from surface waters. However, very little ...N2‐fixation research has focused on the South Atlantic Gyre, where dust deposition of iron (Fe), an important micronutrient for diazotrophs, is seasonally low. Recent modeling efforts suggest that N2‐fixation may in fact be closely coupled to, and greatest in, areas of denitrification, as opposed to the oceanic gyres. One of these areas, the Benguela Upwelling System, lies to the east of the South Atlantic Gyre. In this study we show that N2‐fixation in surface waters across the South Atlantic Gyre was low overall (<1.5 nmol N l−1 d−1) with highest rates seen in or near the Benguela Upwelling System (up to ∼8 nmol N l−1 d−1). Surface water dissolved Fe (dFe) concentrations were very low in the gyre (∼0.3 nM or lower), while soluble reactive phosphorus (SRP) concentrations were relatively high (∼0.15 μM). N2‐fixation rates across the entire sampling area were significantly positively correlated to dFe, but also to SRP and NO3−. Thus, high NO3− concentrations did not exclude N2‐fixation in the upwelling region, which provides evidence that N2‐fixation may be occurring in previously unrecognized waters, specifically near denitrification zones. However the gene encoding for a nitrogenase component (nifH) was not detected from known diazotrophs at some stations in or near the upwelling where N2‐fixation was greatest, suggesting the presence of unknown diazotrophs in these waters.
Key Points
N2 fixation was found in the Benguela Upwelling System
Heterotrophic diazotrophs may be responsible
Iron (but not nitrate) concentrations appear to be a driver of activity
While the ecological role that Trichodesmium sp. play in nitrogen fixation has been widely studied, little information is available on potential specialized metabolites that are associated with ...blooms and standing stock Trichodesmium colonies. While a collection of biological material from a T. thiebautii bloom event from North Padre Island, Texas, in 2014 indicated that this species was a prolific producer of chlorinated specialized metabolites, additional spatial and temporal resolution was needed. We have completed these metabolite comparison studies, detailed in the current report, utilizing LC-MS/MS-based molecular networking to visualize and annotate the specialized metabolite composition of these Trichodesmium blooms and colonies in the Gulf of Mexico (GoM) and other waters. Our results showed that T. thiebautii blooms and colonies found in the GoM have a remarkably consistent specialized metabolome. Additionally, we isolated and characterized one new macrocyclic compound from T. thiebautii, trichothilone A (1), which was also detected in three independent cultures of T. erythraeum. Genome mining identified genes predicted to synthesize certain functional groups in the T. thiebautii metabolites. These results provoke intriguing questions of how these specialized metabolites affect Trichodesmium ecophysiology, symbioses with marine invertebrates, and niche development in the global oligotrophic ocean.
Cobalt (Co) is a scarce but essential micronutrient for marine plankton in
the Southern Ocean and coastal Antarctic seas, where dissolved cobalt (dCo)
concentrations can be extremely low. This study ...presents total dCo and
labile dCo distributions measured via shipboard voltammetry in the Amundsen
Sea, the Ross Sea and Terra Nova Bay during the CICLOPS (Cobalamin and Iron
Co-Limitation of Phytoplankton Species) expedition. A significantly smaller
dCo inventory was observed during the 2017/2018 CICLOPS expedition compared
to two 2005/2006 expeditions to the Ross Sea conducted over a decade
earlier. The dCo inventory loss (∼ 10–20 pM) was present in
both the surface and deep ocean and was attributed to the loss of labile
dCo, resulting in the near-complete complexation of dCo by strong ligands in
the photic zone. A changing dCo inventory in Antarctic coastal seas could be
driven by the alleviation of iron (Fe) limitation in coastal areas, where the
flux of Fe-rich sediments from melting ice shelves and deep sediment
resuspension may have shifted the region towards vitamin B12 and/or
zinc (Zn) limitation, both of which are likely to increase the demand for Co
among marine plankton. High demand for Zn by phytoplankton can result in
increased Co and cadmium (Cd) uptake because these metals often share the
same metal uptake transporters. This study compared the magnitudes and
ratios of Zn, Cd and Co uptake (ρ) across upper-ocean profiles and
the observed order-of-magnitude uptake trends (ρZn > ρCd > ρCo) that paralleled the trace metal concentrations in
seawater. High rates of Co and Zn uptake were observed throughout the
region, and the speciation of available Co and Zn appeared to influence
trends in dissolved metal : phosphate stoichiometry and uptake rates over
depth. Multi-year loss of the dCo inventory throughout the water column may
be explained by an increase in Co uptake into particulate organic matter and
subsequently an increased flux of Co into sediments via sinking and burial.
This perturbation of the Southern Ocean Co biogeochemical cycle could signal
changes in the nutrient limitation regimes, phytoplankton bloom composition
and carbon sequestration sink of the Southern Ocean.
We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution ...of peptides during protein inference. Improvements include ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the least common ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal (https://metatryp.whoi.edu). Major expansion of the marine METATRYP database with predicted proteomes from environmental sequencing confirms a low occurrence of shared tryptic peptides among disparate marine microorganisms, implying tractability for targeted metaproteomics. METATRYP was designed to facilitate ocean metaproteomics and has been integrated into the Ocean Protein Portal (https://oceanproteinportal.org); however, it can be readily applied to other domains. We describe the rapid deployment of a coronavirus-specific web portal (https://metatryp-coronavirus.whoi.edu/) to aid in use of proteomics on coronavirus research during the ongoing pandemic. A coronavirus-focused METATRYP database identified potential SARS-CoV-2 peptide biomarkers and indicated very few shared tryptic peptides between SARS-CoV-2 and other disparate taxa analyzed, sharing <1% peptides with taxa outside of the betacoronavirus group, establishing that taxonomic specificity is achievable using tryptic peptide-based proteomic diagnostic approaches.
Analysis of conserved protein folding domains across extant genomes by Kim et al. in this issue of Structure provides insights into the timing of some of the earliest aerobic metabolisms to arise on ...Earth.
We evaluated the regional distributions of six nitrogen (N₂)-fixing bacteria in the North Pacific Ocean using quantitative polymerase chain reaction amplification of planktonic nifH genes. Samples ...were collected on four oceanographic research cruises between March 2002 and May 2005 that spanned a latitudinal range from 12°S and 54°N between 152°W and 170°W. Samples were collected throughout the upper ocean (<200 m) in the northern regions of the South Pacific Subtropical Gyre (SPSG), equatorial waters, the North Pacific Subtropical Gyre (NPSG), the North Pacific Transitional Zone (NPTZ), and within the Pacific Sub Arctic Gyre (PSAG). There were distinct spatial gradients in concentrations of nutrients, chlorophyll, and the abundances of N₂-fixing bacteria within the various oceanic biomes. In general, nifH-containing bacteria were most abundant in the midregions of the NPSG (latitudes between ~14°N and 29°N), where unicellular cyanobacterial phylotypes dominated nifH gene abundances. The abundances of all nifH-containing groups declined within the northern and southern regions of NPSG. Although nifH-containing groups were detectable in the northern regions of the SPSG, throughout the equatorial waters, and within the NPTZ, gene copy abundances of most groups were lower in these regions than those found the in the NPSG. In the NPSG, surface water abundances of the various nifH phylotypes examined ranged from <50 copies L⁻¹ to ~10⁵ nifH copies L;⁻¹. Overall, the abundances of an uncultivated, presumed unicellular nifH sequence-type (termed Group A) were the most abundant and widely distributed of the phylotypes examined. Our results indicate that the distributions of N₂-fixing plankton were largely restricted to the subtropical regions of the North and South Pacific Oceans.
is a major dinitrogen (N
)-fixing microorganism, providing bioavailable nitrogen (N) to marine ecosystems. The N
-fixing enzyme nitrogenase is deactivated by oxygen (O
), which is abundant in marine ...environments. Using a cellular scale model of
sp. and laboratory data, we quantify the role of three O
management strategies by
sp.: size adjustment, reduced O
diffusivity, and respiratory protection. Our model predicts that
cells increase their size under high O
Using transmission electron microscopy, we show that starch granules and thylakoid membranes are located near the cytoplasmic membranes, forming a barrier for O
The model indicates a critical role for respiration in protecting the rate of N
fixation. Moreover, the rise in respiration rates and the decline in ambient O
with temperature strengthen this mechanism in warmer water, providing a physiological rationale for the observed niche of
at temperatures exceeding 20°C. Our new measurements of the sensitivity to light intensity show that the rate of N
fixation reaches saturation at a lower light intensity (∼100 μmol m
s
) than photosynthesis and that both are similarly inhibited by light intensities of >500 μmol m
s
This suggests an explanation for the maximum population of
occurring slightly below the ocean surface.
is one of the major N
-fixing microorganisms in the open ocean. On a global scale, the process of N
fixation is important in balancing the N budget, but the factors governing the rate of N
fixation remain poorly resolved. Here, we combine a mechanistic model and both previous and present laboratory studies of
to quantify how chemical factors such as C, N, Fe, and O
and physical factors such as temperature and light affect N
fixation. Our study shows that
combines multiple mechanisms to reduce intracellular O
to protect the O
-sensitive N
-fixing enzyme. Our model, however, indicates that these protections are insufficient at low temperature due to reduced respiration and the rate of N
fixation becomes severely limited. This provides a physiological explanation for why the geographic distribution of
is confined to the warm low-latitude ocean.
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