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DOE OSTI2025

Diel partitioning in microbial phosphorus acquisition in the Sargasso Sea

The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. Microbial competition for these scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. In conclusion, these results support the generality of temporal niche partitioning as an emergent mechanism that can structure uptake of limiting nutrients and facilitate coexistence of diverse microbes in open ocean ecosystems.

biological oceanography↗

DOE OSTI2025

Ecosystem consequences of a nitrogen-fixing proto-organelle

Microscale symbioses can be critical to ecosystem functions, but the mechanisms of these interactions in nature are often cryptic. Here, we use a combination of stable isotope imaging and tracing to reveal carbon (C) and nitrogen (N) exchanges among three symbiotic primary producers that fuel a salmon-bearing river food web. Bulk isotope analysis, nanoSIMS (secondary ion mass spectrometry) isotope imaging, and density centrifugation for quantitative stable isotope probing enabled quantification of organism-specific C- and N-fixation rates from the subcellular scale to the ecosystem. After winters with riverbed-scouring floods, the macroalga Cladophora glomerata uses nutrients in spring runoff to grow streamers up to 10 m long. During summer flow recession, riverine N concentrations wane and Cladophora becomes densely epiphytized by three species of Epithemia, diatoms with N-fixing endosymbionts (proto-organelles) descended from a free-living Crocosphaera cyanobacterium. Over summertime epiphyte succession on Cladophora, N-fixation rates increased as Epithemia spp. became dominant, Cladophora C-fixation declined to near zero, and Epithemia C-fixation increased. Carbon transfer to caddisflies grazing on Cladophora with high densities of Epithemia was 10-fold higher than C transfer to caddisflies grazing Cladophora with low Epithemia loads. In response to demand for N, Epithemia allocates high levels of newly fixed C to its endosymbiont. Consequently, these endosymbionts have the highest rates of C and N accumulation of any taxon in this tripartite symbiosis during the biologically productive season and can produce one of the highest areal rates of N-fixation reported in any river ecosystem.

Marks, Jane C. [Northern Arizona Univ., Flagstaff,↗

DOE OSTI2021

Role of uncertainties in protecting ecological resources during remediation and restoration

Cleanup of contaminated waste sites is a National priority to protect human health and the environment, while restoring land to productive uses. While there are uncertainties with under standing risk to individuals from exposure, the aim of this study was to focus on uncertainties and complexities for ecological systems, complicated by hundreds of species occupying any remediation site which participate in multiple-interacting food webs. The ability to better predict the effectiveness of remediation in fostering future ecosystems might facilitate remedy selection and improve strategic environmental management. This investigation examined (1) uncertainties in ecosystem processes, (2) uncertainties in exposure from contamination before remediation, and (3) uncertainties during remediation. Two Department of Energy sites Hanford Site and Savannah River Site were used as case studies to illustrate how the uncertainties affect eco-receptors. Several types of ecological, physical, and human dimension uncertainties are defined. Ecological uncertainties include temporal, spatial, individual, developmental, and exogenous types. Physical uncertainties are weather-related, watershed variations, slope/aspect, soil/sediment structure and form, unforeseen events, and temporal patterns. Human dimension uncertainties include current land use, future land use, extractive and non-extractive recreation. The effects of remedial strategies varied between the two sites because Hanford is a primarily arid shrub-steppe ecotype, while Savannah River is a wet forest ecotype. Defining the associated ecological sensitivities and uncertainties and providing examples might help policy-makers, managers, planners, and contractors to be aware of issues to consider throughout planning, remediation, and restoration. Adding ecological uncertainty analysis to risk evaluations and remediation planning is analogous to using safety factors in human health risk assessment.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Increasing freshwater and dissolved organic carbon flows to Northwest Alaska’s Elson lagoon

Manifestations of climate change in the Arctic are numerous and include hydrological cycle intensification and permafrost thaw, both expected as a result of atmospheric and surface warming. Across the terrestrial Arctic dissolved organic carbon (DOC) entrained in arctic rivers may be providing a carbon subsidy to coastal food webs. Yet, data from field sampling is too often of limited duration to confidently ascertain impacts of climate change on freshwater and DOC flows to coastal waters. This study applies numerical modeling to investigate trends in freshwater and DOC exports from land to Elson Lagoon in Northwest Alaska over the period 1981-2020. While the modeling approach has limitations, the results point to significant increases in freshwater and DOC exports to the lagoon over the past four decades. The model simulation reveals significant increases in surface, subsurface (suprapermafrost), and total freshwater exports. Significant increases are also noted in surface and subsurface DOC production and export, influenced by warming soils and associated active-layer thickening. The largest changes in subsurface components are noted in September, which has experienced a ~50% increase in DOC export emanating from suprapermafrost flow. Direct coastal suprapermafrost freshwater and DOC exports in late summer more than doubled between the first and last five years of the simulation period, with a large anomaly in September 2019 representing a more than fourfold increase over September direct coastal export during the early 1980s. These trends highlight the need for dedicated measurement programs that will enable improved understanding of climate change impacts on coastal zone processes in this data sparse region of Northwest Alaska.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Insights into the year-round vertical distribution of chlorophyll concentration in high-latitude Arctic Ocean: implications for primary production

Climate-induced rapid changes in the Arctic Ocean, such as decreasing sea ice extent and increasing water temperature, are altering nutrient and light availability, profoundly impacting primary producer growth. However, access to the high-latitude Arctic Ocean is limited, and satellite data are primarily available only during summer, making continuous in-situ data collection challenging. We collected year-round chlorophyll-a (Chl-a) concentration data in high-latitude regions using a mooring system and performed a comparative analysis with reanalysis data. Unlike previous satellite-based studies, which typically rely on surface measurements, we used the annual vertical distribution of Chl-a. These data were applied to the vertically generalized production model to accurately estimate annual primary production. The moored Chl-a concentration data showed that phytoplankton exhibited a typical subsurface chlorophyll maximum (SCM) layer as sea ice retreated in June. Contrary to the gradually deepening SCM distribution predicted by model-based reanalysis data, the SCM layer persisted for approximately 4 months. This indicates that light and nutrient conditions within the SCM layer remained stable, sustaining continuous phytoplankton growth. Annual primary production, reflecting this vertical distribution of Chl-a concentration, was 6.85 gC m −2 yr −1 . This exceeded satellite-based estimates by at least two-fold, highlighting the significant underestimation of primary production by satellite approaches. Estimating primary production while accounting for the vertical distribution of phytoplankton and light is essential for improving ecological models to better understand carbon cycle and food web changes in the Arctic Ocean, with important implications for climate change predictions.

Arctic Ocean↗

DOE OSTI2021

Climate-Mediated Changes to Linked Terrestrial and Marine Ecosystems across the Northeast Pacific Coastal Temperate Rainforest Margin

Coastal margins are important areas of materials flux that link terrestrial and marine ecosystems. Consequently, climate-mediated changes to coastal terrestrial ecosystems and hydrologic regimes have high potential to influence nearshore ocean chemistry and food web dynamics. Research from tightly coupled, high-flux coastal ecosystems can advance understanding of terrestrial–marine links and climate sensitivities more generally. In the present article, we use the northeast Pacific coastal temperate rainforest as a model system to evaluate such links. We focus on key above- and belowground production and hydrological transport processes that control the land-to-ocean flow of materials and their influence on nearshore marine ecosystems. We evaluate how these connections may be altered by global climate change and we identify knowledge gaps in our understanding of the source, transport, and fate of terrestrial materials along this coastal margin. Finally, we propose five priority research themes in this region that are relevant for understanding coastal ecosystem links more broadly.

temperate rainforest, coastal margin, climate chan↗

DOE OSTI2020

Fungi and viruses as important players in microbial mats

ABSTRACT Microbial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.

Carreira, Cátia↗

DOE OSTI2025

Spatially structured bacterial interactions alter algal carbon flow to bacteria

Phytoplankton account for nearly half of global photosynthetic carbon fixation, and the fate of that carbon is regulated in large part by microbial food web processing. We currently lack a mechanistic understanding of how interactions among heterotrophic bacteria impact the fate of photosynthetically fixed carbon. Here, we used a set of bacterial isolates capable of growing on exudates from the diatom Phaeodactylum tricornutum to investigate how bacteria-bacteria interactions affect the balance between exudate remineralization and incorporation into biomass. With exometabolomics and genome-scale metabolic modeling, we estimated the degree of resource competition between bacterial pairs. In a sequential spent media experiment, we found that pairwise interactions were more beneficial than predicted based on resource competition alone, and 30% exhibited facilitative interactions. To link this to carbon fate, we used single-cell isotope tracing in a custom cultivation system to compare the impact of different "primary" bacterial strains in close proximity to live P. tricornutum on a distal "secondary" strain. We found that a primary strain with a high degree of competition decreased secondary strain carbon drawdown by 51% at the single-cell level, providing a quantitative metric for the "cost" of competition on algal carbon fate. Additionally, a primary strain classified as facilitative based on sequential interactions increased total algal-derived carbon assimilation by 7.6 times, integrated over all members, compared to the competitive primary strain. Our findings suggest that the degree of interaction between bacteria along a spectrum from competitive to facilitative is directly linked to algal carbon drawdown.

genome-scale metabolic model↗

DOE OSTI2022

Mycorrhiza‐induced mycocypins of Laccaria bicolor are potent protease inhibitors with nematotoxic and collembola antifeedant activity

Fungivory of mycorrhizal hyphae has a significant impact on fungal fitness and, by extension, on nutrient transfer between fungi and host plants in natural ecosystems. Mycorrhizal fungi have therefore evolved an arsenal of chemical compounds that are hypothesized to protect the hyphal tissues from being eaten, such as the protease inhibitors mycocypins. The genome of the ectomycorrhizal fungus Laccaria bicolor has an unusually high number of mycocypin-encoding genes. We have characterized the evolution of this class of proteins, identified those induced by symbiosis with a host plant and characterized the biochemical properties of two upregulated L. bicolor mycocypins. More than half of L. bicolor mycocypin-encoding genes are differentially expressed during symbiosis or fruiting body formation. We show that two L. bicolor mycocypins that are strongly induced during symbiosis are cysteine protease inhibitors and exhibit similar but distinct localization in fungal tissues at different developmental stages and during interaction with a host plant. Moreover, we show that these L. bicolor mycocypins have toxic and feeding deterrent effect on nematodes and collembolans, respectively. Therefore, L. bicolor mycocypins may be part of a mechanism by which this species deters grazing by different members of the soil food web.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Protistan community composition and metabolism in the North Pacific Subtropical Gyre: Influences of mesoscale eddies and depth

Abstract Marine protists and their metabolic activities are intricately tied to the cycling of nutrients and the flow of energy through microbial food webs. Physiochemical changes in the environment, such as those that result from mesoscale eddies, may impact protistan communities, but the effects that such changes have on protists are poorly known. A metatranscriptomic study was conducted to investigate how eddies affected protists at adjacent cyclonic and anticyclonic eddy sites in the oligotrophic ocean at four depths from 25 to 250 m. Eddy polarity impacted protists at all depths sampled, although the effects of eddy polarity were secondary to the impact of depth across the depth range. Eddy‐induced vertical shifts in the water column yielded differences in the cyclonic and anticyclonic eddy protistan communities, and these differences were the most pronounced at and just below the deep chlorophyll maximum. An analysis of transcripts associated with protistan nutritional physiology at 150 m revealed that cyclonic eddies may support a more heterotrophic community, while anticyclonic eddies promote a more phototrophic community. The results of this study indicate that eddies alter the metabolism of protists particularly in the lower euphotic zone and may therefore impact carbon export from the euphotic zone.

Microbiology↗

DOE OSTI2025

Surface Texture of Macroplastic Pollution in Streams Alters the Physical Structure and Diversity of Biofilm Communities

ABSTRACT Biofilms can develop on nearly any surface, and in aquatic ecosystems they are essential components of biogeochemical cycles and food webs. Plastic waste in waterways is a new type of surface for biofilm colonisation. To analyse the influence of plastic pollution on the development and diversity of microbial freshwater biofilms that colonised them, we incubated 388 cm 2 veneers of high‐density polyethylene (HDPE) with two veneer textures, smooth and rough, and tulip tree wood ( Liriodendron tulipifera ), in three rural headwater streams at the Savannah River Site (Aiken, SC, USA). We collected biofilms from veneers after 14, 28 and 56 days of incubation and analysed 16S rRNA genes and biofilm properties. We found that plastic negatively affected species richness of biofilms compared with wood, but that evenness was greatest on rough textured HDPE. Beta diversity was primarily influenced by stream site. Beta diversity differed more between wood and plastic veneers than with plastic surface texture and became more different over time. Wood had nine times more biomass than rough HDPE and 40 times more biomass than smooth HDPE. Given the projected increase of macroplastic pollution in aquatic ecosystems, our findings emphasise the need to further understand its effects on biofilm characteristics.

Lopez Avila, Fabiola [Odum School of Ecology Unive↗

DOE OSTI2023

Community size-spectra applied to recreational freshwater fisheries in Puerto Rican reservoirs

We developed a management framework based on community size-spectra (CSS) to establish targets to maximize desirable gamefish. We evaluated the influence of relative abundance of fish functional groups and watershed characteristics on the slope of the CSS or ecological efficiency. Both ecological efficiency and capacity were strongly influenced by relative abundance of fish functional groups and the degree of water level variation. Steeper slopes indicated overfished gamefish populations, whereas flatter slopes indicated systems dominated by undesirable invasive large-bodied low trophic position fish. We hypothesize that a desirable fishery would have a target range of CSS slopes that provides a deterministic community-based framework of predictable responses to environmental and food web changes that can be used to evaluate outcomes of management actions and a means to assess annual progress toward desirable conditions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Temperature and CO 2 interactively drive shifts in the compositional and functional structure of peatland protist communities

Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long-term whole-ecosystem warming experiment at a boreal peatland to answer how temperature and CO 2 jointly influence communities of abundant, diverse, yet poorly understood, non-fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria and fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report large climate-induced, community-wide shifts in the community functional composition of these microbes (size, shape, and metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO 2 with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO 2 and amplified in larger microbes but not smaller ones. Furthermore, these findings show how the interactive effects of warming and rising CO 2 levels could alter the structure and function of peatland microbial food webs—a fragile ecosystem that stores upwards of 25% of all terrestrial carbon and is increasingly threatened by human exploitation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

The diatom Fragilariopsis cylindrus : A model alga to understand cold-adapted life

Diatoms are significant primary producers especially in cold, turbulent, and nutrient-rich surface oceans. Hence, they are abundant in polar oceans, but also underpin most of the polar food webs and related biogeochemical cycles. The cold-adapted pennate diatom Fragilariopsis cylindrus is considered a keystone species in polar oceans and sea ice because it can thrive under different environmental conditions if temperatures are low. In this perspective paper, we provide insights into the latest molecular work that has been done on F. cylindrus and discuss its role as a model alga to understand cold-adapted life.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Transcriptional Control of hgcAB by an ArsR-Like Regulator in Pseudodesulfovibrio mercurii ND132

The hgcAB gene pair encodes mercury (Hg) methylation capability in a diverse group of microorganisms, but its evolution and transcriptional regulation remain unknown. Working from the possibility that the evolutionary function of HgcAB may not be Hg methylation, we test a possible link to arsenic resistance. Using model Hg methylator Pseudodesulfovibrio mercurii ND132, we evaluated transcriptional control of hgcAB by a putative ArsR encoded upstream and cotranscribed with hgcAB. This regulator shares homology with ArsR repressors of arsenic resistance and S-adenosylhomocysteine (SAH)- responsive regulators of methionine biosynthesis but is distinct from other ArsR/SahR proteins in P. mercurii. Using quantitative PCR (qPCR) and RNA sequencing (RNA-seq) transcriptome analyses, we confirmed this ArsR regulates hgcAB transcription and is responsive to arsenic and SAH. Additionally, RNA-seq indicated a possible link between hgcAB activity and arsenic transformations, with significant upregulation of other ArsRregulated arsenic resistance operons alongside hgcAB. Interestingly, wild-type ND132 was less sensitive to As(V) (but not As(III)) than an hgcAB knockout strain, supporting the idea that hgcAB may be linked to arsenic resistance. Arsenic significantly impacted rates of Hg methylation by ND132; however, responses varied with culture conditions. Differences in growth and metabolic activity did not account for arsenic impacts on methylation. While arsenic significantly increased hgcAB expression, hgcAB gene and transcript abundance was not a good predictor of Hg methylation rates. Taken together, these results support the idea that Hg and As cycling are linked in P. mercurii ND132. Our results may hold clues to the evolution of hgcAB and the controls on Hg methylation in nature. This work reveals a link between microbial mercury methylation and arsenic resistance and may hold clues to the evolution of mercury methylation genes (hgcAB). Microbes with hgcAB produce methylmercury, a strong neurotoxin that readily accumulates in the food web. This study addresses a critical gap in our understanding about the environmental factors that control hgcAB expression. We show that hgcAB expression is controlled by an ArsR-like regulator responsive to both arsenic and S-adenosylhomocysteine in our model organism, Pseudodesulfovibrio mercurii ND132. Exposure to arsenic also significantly impacted Pseudodesulfovibrio mercurii ND132 mercury methylation rates. However, expression of hgcAB was not always a good predictor of Hg methylation rates, highlighting the roles of Hg bioavailability and other biochemical mechanisms in methylmercury production. This study improves our understanding of the controls on hgcAB expression, which is needed to better predict environmental methylmercury production

RNA-seq↗

DOE OSTI2023

Giant Virus Infection Signatures Are Modulated by Euphotic Zone Depth Strata and Iron Regimes of the Subantarctic Southern Ocean

Viruses can alter the abundance, evolution, and metabolism of microorganisms in the ocean, playing a key role in water column biogeochemistry and global carbon cycles. Large efforts to measure the contribution of eukaryotic microorganisms (e.g., protists) to the marine food web have been made, yet the in situ activities of the ecologically relevant viruses that infect these organisms are not well characterized. Viruses within the phylum Nucleocytoviricota (“giant viruses”) are known to infect a diverse range of ecologically relevant marine protists, yet how these viruses are influenced by environmental conditions remains under-characterized. By employing metatranscriptomic analyses of in situ microbial communities along a temporal and depthresolved gradient, we describe the diversity of giant viruses at the Southern Ocean Time Series (SOTS), a site within the subpolar Southern Ocean. Using a phylogeny-guided taxonomic assessment of detected giant virus genomes and metagenome-assembled genomes, we observed depth-dependent structuring of divergent giant virus families mirroring dynamic physicochemical gradients in the stratified euphotic zone. Analyses of transcribed metabolic genes from giant viruses suggest viral metabolic reprogramming of hosts from the surface to a 200-m depth. Lastly, using on-deck incubations reflecting a gradient of iron availability, we show that modulating iron regimes influences the activity of giant viruses in the field. Specifically, we show enhanced infection signatures of giant viruses under both iron-replete and iron-limited conditions. Collectively, these results expand our understanding of how the water column’s vertical biogeography and chemical surroundings affect an important group of viruses within the Southern Ocean

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Earth, Wind, Fire, and Pollution: Aerosol Nutrient Sources and Impacts on Ocean Biogeochemistry

A key Earth system science question is the role of atmospheric deposition in supplying vital nutrients to the phytoplankton that form the base of marine food webs. Industrial and vehicular pollution, wildfires, volcanoes, biogenic debris, and desert dust all carry nutrients within their plumes throughout the globe. In remote ocean ecosystems, aerosol deposition represents an essential new source of nutrients for primary production. The large spatiotemporal variability in aerosols from myriad sources combined with the differential responses of marine biota to changing fluxes makes it crucially important to understand where, when, and how much nutrients from the atmosphere enter marine ecosystems. This review brings together existing literature, experimental evidence of impacts, and new atmospheric nutrient observations that can be compared with atmospheric and ocean biogeochemistry modeling. We evaluate the contribution and spatiotemporal variability of nutrient-bearing aerosols from desert dust, wildfire, volcanic, and anthropogenic sources, including the organic component, deposition fluxes, and oceanic impacts.

Marine & Freshwater Biology↗

DOE OSTI2022

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans

Abstract Background Phytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genomes (MAGs), this approach has yet to be applied for complex phytoplankton microbiomes from polar and non-polar oceans consisting of microbial eukaryotes and their associated prokaryotes. Results Here, we have assembled MAGs from chlorophyll a maximum layers in the surface of the Arctic and Atlantic Oceans enriched for species associations (microbiomes) with a focus on pico- and nanophytoplankton and their associated heterotrophic prokaryotes. From 679 Gbp and estimated 50 million genes in total, we recovered 143 MAGs of medium to high quality. Although there was a strict demarcation between Arctic and Atlantic MAGs, adjacent sampling stations in each ocean had 51–88% MAGs in common with most species associations between Prasinophytes and Proteobacteria . Phylogenetic placement revealed eukaryotic MAGs to be more diverse in the Arctic whereas prokaryotic MAGs were more diverse in the Atlantic Ocean. Approximately 70% of protein families were shared between Arctic and Atlantic MAGs for both prokaryotes and eukaryotes. However, eukaryotic MAGs had more protein families unique to the Arctic whereas prokaryotic MAGs had more families unique to the Atlantic. Conclusion Our study provides a genomic context to complex phytoplankton microbiomes to reveal that their community structure was likely driven by significant differences in environmental conditions between the polar Arctic and warm surface waters of the tropical and subtropical Atlantic Ocean.

59 BASIC BIOLOGICAL SCIENCES↗