Surpassing natural limits in one-carbon assimilation
Related Articles
Single cell dynamics and nitrogen transformations in the chain forming diatom Chaetoceros affinis
Colony formation in phytoplankton is often considered a disadvantage during nutrient limitation in aquatic systems. Using stable isotopic tracers combined with secondary ion mass spectrometry (SIMS), we unravel cell-specific activities of a chain-forming diatom and interactions with attached bacteria. The uptake of 13C-bicarbonate and15N-nitrate or 15N-ammonium was studied in Chaetoceros affinis during the stationary growth phase. Low cell-to-cell variance of 13C-bicarbonate and 15N-nitrate assimilation within diatom chains prevailed during the early stationary phase. Up to 5% of freshly assimilated 13C and 15N was detected in attached bacteria within 12 h and supported bacterial C- and N-growth rates up to 0.026 h−1. During the mid-stationary phase, diatom chain-length decreased and 13C and 15N-nitrate assimilation was significantly higher in solitary cells as compared to that in chain cells. During the late stationary phase, nitrate assimilation ceased and ammonium assimilation balanced C fixation. At this stage, we observed highly active cells neighboring inactive cells within the same chain. In N-limited regimes, bacterial remineralization of N and the short diffusion distance between neighbors in chains may support surviving cells. This combination of “microbial gardening” and nutrient transfer within diatom chains represents a strategy which challenges current paradigms of nutrient fluxes in plankton communities.
Temperature-driven nitrogen mixotrophy shapes marine cyanobacteria Prochlorococcus and Synechococcus latitudinal distribution pattern
Temperature, photosynthetically active radiation, and nutrient availability are pivotal in determining the global distribution of marine cyanobacteria. This study demonstrates that the distinct latitudinal niches of Synechococcus and Prochlorococcus are modulated by their temperature-dependent, mixotrophic nitrogen utilization strategies. Comparative genomic analysis reveals that Prochlorococcus ecotypes differ in their nitrogen transporter repertoire, with low-light ecotypes harboring ~12 transporters, while high-light ecotypes possess ~5 transporters. Conversely, Synechococcus displays greater genomic flexibility, with 17 nitrogen transporters. Reanalysis of Tara Oceans metatranscriptomic data identifies ~15 °C as a key thermal threshold for cyanobacterial distribution. In warmer regions (15-30°C, 35˚S-40˚N), Prochlorococcus optimizes nitrogen transporter functions across their ecotypes, whereas Synechococcus, leveraging its broad nitrogen transporters, exhibits functional plasticity, utilizing inorganic nitrogen in warmer waters and organic nitrogen in cooler waters ranging from -2°C to 15 °C beyond 35˚S/40˚N. Our findings underscore the critical role of temperature-driven mixotrophic nitrogen utilization in shaping the biogeographical patterns of marine cyanobacteria.
Synechococcus nitrogen gene loss in iron-limited ocean regions
Synechococcus are the most abundant cyanobacteria in high latitude regions and are responsible for an estimated 17% of annual marine net primary productivity. Despite their biogeochemical importance, Synechococcus populations have been unevenly sampled across the ocean, with most studies focused on low-latitude strains. In particular, the near absence of Synechococcus genomes from high-latitude, High Nutrient Low Chlorophyll (HNLC) regions leaves a gap in our knowledge of picocyanobacterial adaptations to iron limitation and their influence on carbon, nitrogen, and iron cycles. We examined Synechococcus populations from the subarctic North Pacific, a well-characterized HNLC region, with quantitative metagenomics. Assembly with short and long reads produced two near complete Synechococcus metagenome-assembled genomes (MAGs). Quantitative metagenome-derived abundances of these populations matched well with flow cytometry counts, and the Synechococcus MAGs were estimated to comprise >99% of the Synechococcus at Station P. Whereas the Station P Synechococcus MAGs contained multiple genes for adaptation to iron limitation, both genomes lacked genes for uptake and assimilation of nitrate and nitrite, suggesting a dependence on ammonium, urea, and other forms of recycled nitrogen leading to reduced iron requirements. A global analysis of Synechococcus nitrate reductase abundance in the TARA Oceans dataset found nitrate assimilation genes are also lower in other HNLC regions. We propose that nitrate and nitrite assimilation gene loss in Synechococcus may represent an adaptation to severe iron limitation in high-latitude regions where ammonium availability is higher. Our findings have implications for models that quantify the contribution of cyanobacteria to primary production and subsequent carbon export.
Rising greenhouse gas emissions embodied in the global bioeconomy supply chain
The bioeconomy is key to meeting climate targets. Here, we examine greenhouse gas emissions in the global bioeconomy supply chain (1995–2022) using advanced multi-regional input-output analysis and a global land-use change model. Considering agriculture, forestry, land use, and energy, we assess the carbon footprint of biomass production and examine its end-use by provisioning systems. The footprint increased by 3.3 Gt CO2-eq, with 80% driven by international trade, mainly beef and biochemicals (biofuels, bioplastics, rubber). Biochemicals showed the largest relative increase, doubling due to tropical land-use change (feedstock cultivation) and China’s energy-intensive processing. Food from retail contributes most to the total biomass carbon footprint, while food from restaurants and canteens account for >50% of carbon-footprint growth, with three times higher carbon intensity than retail. Our findings emphasize the need for sustainable sourcing strategies and that adopting renewables and halting land-use change could reduce the bioeconomy carbon footprint by almost 60%.
Resource partitioning and amino acid assimilation in a terrestrial geothermal spring
High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.
Responses