Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.

Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2. By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions for ensemble of parameter sets and found no physiological benefit of a model assuming phycobilisome detachment. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. We suggest gene targets for overexpression under different illuminations to increase the yield. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.

Recent decline in tropical temperature sensitivity of atmospheric CO2 growth rate variability.

A two-fold enhancement in the sensitivity of atmospheric CO2 growth rate (CGR) to tropical temperature interannual variability ( Γ CGR T $$ {\varGamma}_{\mathrm{CGR}}^T $$ ) till early 2000s has been reported, which suggests a drought-induced shift in terrestrial carbon cycle responding temperature fluctuations, thereby accelerating global warming. However, using six decades long atmospheric CO2 observations, we show that Γ CGR T $$ {\varGamma}_{\mathrm{CGR}}^T $$ has significantly declined in the last two decades, to the level during the 1960s. The Γ CGR T $$ {\varGamma}_{\mathrm{CGR}}^T $$ decline begs the question of whether the sensitivity of ecosystem carbon cycle to temperature variations at local scale has largely decreased. With state-of-the-art dynamic global vegetation models, we further find that the recent Γ CGR T $$ {\varGamma}_{\mathrm{CGR}}^T $$ decline is barely attributed to ecosystem carbon cycle response to temperature fluctuations at local scale, which instead results from a decrease in spatial coherence in tropical temperature variability and land use change. Our results suggest that the recently reported loss of rainforest resilience has not shown marked influence on the temperature sensitivity of ecosystem carbon cycle. Nevertheless, the increasing extent of land use change as well as more frequent and intensive drought events are likely to modulate the responses of ecosystem carbon cycle to temperature variations in the future. Therefore, our study highlights the priority to continuously monitor the temperature sensitivity of CGR variability and improve Earth system model representation on land use change, in order to predict the carbon-climate feedback.

Variability of ecosystem carbon source from microbial respiration is controlled by rainfall dynamics.

Soil heterotrophic respiration (Rh) represents an important component of the terrestrial carbon cycle that affects whether ecosystems function as carbon sources or sinks. Due to the complex interactions between biological and physical factors controlling microbial growth, Rh is uncertain and difficult to predict, limiting our ability to anticipate future climate trajectories. Here we analyze the global FLUXNET 2015 database aided by a probabilistic model of microbial growth to examine the ecosystem-scale dynamics of Rh and identify primary predictors of its variability. We find that the temporal variability in Rh is consistently distributed according to a Gamma distribution, with shape and scale parameters controlled only by rainfall characteristics and vegetation productivity. This distribution originates from the propagation of fast hydrologic fluctuations on the slower biological dynamics of microbial growth and is independent of biome, soil type, and microbial physiology. This finding allows us to readily provide accurate estimates of the mean Rh and its variance, as confirmed by a comparison with an independent global dataset. Our results suggest that future changes in rainfall regime and net primary productivity will significantly alter the dynamics of Rh and the global carbon budget. In regions that are becoming wetter, Rh may increase faster than net primary productivity, thereby reducing the carbon storage capacity of terrestrial ecosystems.

Widespread decline in winds delayed autumn foliar senescence over high latitudes.

The high northern latitudes (>50°) experienced a pronounced surface stilling (i.e., decline in winds) with climate change. As a drying factor, the influences of changes in winds on the date of autumn foliar senescence (DFS) remain largely unknown and are potentially important as a mechanism explaining the interannual variability of autumn phenology. Using 183,448 phenological observations at 2,405 sites, long-term site-scale water vapor and carbon dioxide flux measurements, and 34 y of satellite greenness data, here we show that the decline in winds is significantly associated with extended DFS and could have a relative importance comparable with temperature and precipitation effects in contributing to the DFS trends. We further demonstrate that decline in winds reduces evapotranspiration, which results in less soil water losses and consequently more favorable growth conditions in late autumn. In addition, declining winds also lead to less leaf abscission damage which could delay leaf senescence and to a decreased cooling effect and therefore less frost damage. Our results are potentially useful for carbon flux modeling because an improved algorithm based on these findings projected overall widespread earlier DFS than currently expected by the end of this century, contributing potentially to a positive feedback to climate.

Multiple constraints cause positive and negative feedbacks limiting grassland soil CO2 efflux under CO2 enrichment.

Terrestrial ecosystems are increasingly enriched with resources such as atmospheric CO2 that limit ecosystem processes. The consequences for ecosystem carbon cycling depend on the feedbacks from other limiting resources and plant community change, which remain poorly understood for soil CO2 efflux, JCO2, a primary carbon flux from the biosphere to the atmosphere. We applied a unique CO2 enrichment gradient (250 to 500 µL L-1) for eight years to grassland plant communities on soils from different landscape positions. We identified the trajectory of JCO2 responses and feedbacks from other resources, plant diversity [effective species richness, exp(H)], and community change (plant species turnover). We found linear increases in JCO2 on an alluvial sandy loam and a lowland clay soil, and an asymptotic increase on an upland silty clay soil. Structural equation modeling identified CO2 as the dominant limitation on JCO2 on the clay soil. In contrast with theory predicting limitation from a single limiting factor, the linear JCO2 response on the sandy loam was reinforced by positive feedbacks from aboveground net primary productivity and exp(H), while the asymptotic JCO2 response on the silty clay arose from a net negative feedback among exp(H), species turnover, and soil water potential. These findings support a multiple resource limitation view of the effects of global change drivers on grassland ecosystem carbon cycling and highlight a crucial role for positive or negative feedbacks between limiting resources and plant community structure. Incorporating these feedbacks will improve models of terrestrial carbon sequestration and ecosystem services.

Decreasing Phanerozoic extinction intensity as a consequence of Earth surface oxygenation and metazoan ecophysiology.

The decline in background extinction rates of marine animals through geologic time is an established but unexplained feature of the Phanerozoic fossil record. There is also growing consensus that the ocean and atmosphere did not become oxygenated to near-modern levels until the mid-Paleozoic, coinciding with the onset of generally lower extinction rates. Physiological theory provides us with a possible causal link between these two observations-predicting that the synergistic impacts of oxygen and temperature on aerobic respiration would have made marine animals more vulnerable to ocean warming events during periods of limited surface oxygenation. Here, we evaluate the hypothesis that changes in surface oxygenation exerted a first-order control on extinction rates through the Phanerozoic using a combined Earth system and ecophysiological modeling approach. We find that although continental configuration, the efficiency of the biological carbon pump in the ocean, and initial climate state all impact the magnitude of modeled biodiversity loss across simulated warming events, atmospheric oxygen is the dominant predictor of extinction vulnerability, with metabolic habitat viability and global ecophysiotype extinction exhibiting inflection points around 40% of present atmospheric oxygen. Given this is the broad upper limit for estimates of early Paleozoic oxygen levels, our results are consistent with the relative frequency of high-magnitude extinction events (particularly those not included in the canonical big five mass extinctions) early in the Phanerozoic being a direct consequence of limited early Paleozoic oxygenation and temperature-dependent hypoxia responses.

Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits.

Blooms of marine phytoplankton fix complex pools of dissolved organic matter (DOM) that are thought to be partitioned among hundreds of heterotrophic microbes at the base of the food web. While the relationship between microbial consumers and phytoplankton DOM is a key component of marine carbon cycling, microbial loop metabolism is largely understood from model organisms and substrates. Here, we took an untargeted approach to measure and analyze partitioning of four distinct phytoplankton-derived DOM pools among heterotrophic populations in a natural microbial community using a combination of ecogenomics, stable isotope probing (SIP), and proteomics. Each 13C-labeled exudate or lysate from a diatom or a picocyanobacterium was preferentially assimilated by different heterotrophic taxa with specialized metabolic and physiological adaptations. Bacteroidetes populations, with their unique high-molecular-weight transporters, were superior competitors for DOM derived from diatom cell lysis, rapidly increasing growth rates and ribosomal protein expression to produce new relatively high C:N biomass. Proteobacteria responses varied, with relatively low levels of assimilation by Gammaproteobacteria populations, while copiotrophic Alphaproteobacteria such as the Roseobacter clade, with their diverse array of ABC- and TRAP-type transporters to scavenge monomers and nitrogen-rich metabolites, accounted for nearly all cyanobacteria exudate assimilation and produced new relatively low C:N biomass. Carbon assimilation rates calculated from SIP data show that exudate and lysate from two common marine phytoplankton are being used by taxonomically distinct sets of heterotrophic populations with unique metabolic adaptations, providing a deeper mechanistic understanding of consumer succession and carbon use during marine bloom events.

Sensitivity of grassland carbon pools to plant diversity, elevated CO2, and soil nitrogen addition over 19 years.

Whether the terrestrial biosphere will continue to act as a net carbon (C) sink in the face of multiple global changes is questionable. A key uncertainty is whether increases in plant C fixation under elevated carbon dioxide (CO2) will translate into decades-long C storage and whether this depends on other concurrently changing factors. We investigated how manipulations of CO2, soil nitrogen (N) supply, and plant species richness influenced total ecosystem (plant + soil to 60 cm) C storage over 19 y in a free-air CO2 enrichment grassland experiment (BioCON) in Minnesota. On average, after 19 y of treatments, increasing species richness from 1 to 4, 9, or 16 enhanced total ecosystem C storage by 22 to 32%, whereas N addition of 4 g N m-2 ⋅ y-1 and elevated CO2 of +180 ppm had only modest effects (increasing C stores by less than 5%). While all treatments increased net primary productivity, only increasing species richness enhanced net primary productivity sufficiently to more than offset enhanced C losses and substantially increase ecosystem C pools. Effects of the three global change treatments were generally additive, and we did not observe any interactions between CO2 and N. Overall, our results call into question whether elevated CO2 will increase the soil C sink in grassland ecosystems, helping to slow climate change, and suggest that losses of biodiversity may influence C storage as much as or more than increasing CO2 or high rates of N deposition in perennial grassland systems.

Microbial dynamics of elevated carbon flux in the open ocean's abyss.

In the open ocean, elevated carbon flux (ECF) events increase the delivery of particulate carbon from surface waters to the seafloor by severalfold compared to other times of year. Since microbes play central roles in primary production and sinking particle formation, they contribute greatly to carbon export to the deep sea. Few studies, however, have quantitatively linked ECF events with the specific microbial assemblages that drive them. Here, we identify key microbial taxa and functional traits on deep-sea sinking particles that correlate positively with ECF events. Microbes enriched on sinking particles in summer ECF events included symbiotic and free-living diazotrophic cyanobacteria, rhizosolenid diatoms, phototrophic and heterotrophic protists, and photoheterotrophic and copiotrophic bacteria. Particle-attached bacteria reaching the abyss during summer ECF events encoded metabolic pathways reflecting their surface water origins, including oxygenic and aerobic anoxygenic photosynthesis, nitrogen fixation, and proteorhodopsin-based photoheterotrophy. The abundances of some deep-sea bacteria also correlated positively with summer ECF events, suggesting rapid bathypelagic responses to elevated organic matter inputs. Biota enriched on sinking particles during a spring ECF event were distinct from those found in summer, and included rhizaria, copepods, fungi, and different bacterial taxa. At other times over our 3-y study, mid- and deep-water particle colonization, predation, degradation, and repackaging (by deep-sea bacteria, protists, and animals) appeared to shape the biotic composition of particles reaching the abyss. Our analyses reveal key microbial players and biological processes involved in particle formation, rapid export, and consumption, that may influence the ocean's biological pump and help sustain deep-sea ecosystems.

Environmental controls on the light use efficiency of terrestrial gross primary production.

Gross primary production (GPP) by terrestrial ecosystems is a key quantity in the global carbon cycle. The instantaneous controls of leaf-level photosynthesis are well established, but there is still no consensus on the mechanisms by which canopy-level GPP depends on spatial and temporal variation in the environment. The standard model of photosynthesis provides a robust mechanistic representation for C3 species; however, additional assumptions are required to "scale up" from leaf to canopy. As a consequence, competing models make inconsistent predictions about how GPP will respond to continuing environmental change. This problem is addressed here by means of an empirical analysis of the light use efficiency (LUE) of GPP inferred from eddy covariance carbon dioxide flux measurements, in situ measurements of photosynthetically active radiation (PAR), and remotely sensed estimates of the fraction of PAR (fAPAR) absorbed by the vegetation canopy. Focusing on LUE allows potential drivers of GPP to be separated from its overriding dependence on light. GPP data from over 100 sites, collated over 20 years and located in a range of biomes and climate zones, were extracted from the FLUXNET2015 database and combined with remotely sensed fAPAR data to estimate daily LUE. Daytime air temperature, vapor pressure deficit, diffuse fraction of solar radiation, and soil moisture were shown to be salient predictors of LUE in a generalized linear mixed-effects model. The same model design was fitted to site-based LUE estimates generated by 16 terrestrial ecosystem models. The published models showed wide variation in the shape, the strength, and even the sign of the environmental effects on modeled LUE. These findings highlight important model deficiencies and suggest a need to progress beyond simple "goodness of fit" comparisons of inferred and predicted carbon fluxes toward an approach focused on the functional responses of the underlying dependencies.

A trait-based understanding of wood decomposition by fungi.

As the primary decomposers of organic material in terrestrial ecosystems, fungi are critical agents of the global carbon cycle. Yet our ability to link fungal community composition to ecosystem functioning is constrained by a limited understanding of the factors accounting for different wood decomposition rates among fungi. Here we examine which traits best explain fungal decomposition ability by combining detailed trait-based assays on 34 saprotrophic fungi from across North America in the laboratory with a 5-y field study comprising 1,582 fungi isolated from 74 decomposing logs. Fungal growth rate (hyphal extension rate) was the strongest single predictor of fungal-mediated wood decomposition rate under laboratory conditions, and accounted for up to 27% of the in situ variation in decomposition in the field. At the individual level, decomposition rate was negatively correlated with moisture niche width (an indicator of drought stress tolerance) and with the production of nutrient-mineralizing extracellular enzymes. Together, these results suggest that decomposition rates strongly align with a dominance-tolerance life-history trade-off that was previously identified in these isolates, forming a spectrum from slow-growing, stress-tolerant fungi that are poor decomposers to fast-growing, highly competitive fungi with fast decomposition rates. Our study illustrates how an understanding of fungal trait variation could improve our predictive ability of the early and midstages of wood decay, to which our findings are most applicable. By mapping our results onto the biogeographic distribution of the dominance-tolerance trade-off across North America, we approximate broad-scale patterns in intrinsic fungal-mediated wood decomposition rates.

Siberian and temperate ecosystems shape Northern Hemisphere atmospheric CO2 seasonal amplification.

The amplitude of the atmospheric CO2 seasonal cycle has increased by 30 to 50% in the Northern Hemisphere (NH) since the 1960s, suggesting widespread ecological changes in the northern extratropics. However, substantial uncertainty remains in the continental and regional drivers of this prominent amplitude increase. Here we present a quantitative regional attribution of CO2 seasonal amplification over the past 4 decades, using a tagged atmospheric transport model prescribed with observationally constrained fluxes. We find that seasonal flux changes in Siberian and temperate ecosystems together shape the observed amplitude increases in the NH. At the surface of northern high latitudes, enhanced seasonal carbon exchange in Siberia is the dominant contributor (followed by temperate ecosystems). Arctic-boreal North America shows much smaller changes in flux seasonality and has only localized impacts. These continental contrasts, based on an atmospheric approach, corroborate heterogeneous vegetation greening and browning trends from field and remote-sensing observations, providing independent evidence for regionally divergent ecological responses and carbon dynamics to global change drivers. Over surface midlatitudes and throughout the midtroposphere, increased seasonal carbon exchange in temperate ecosystems is the dominant contributor to CO2 amplification, albeit with considerable contributions from Siberia. Representing the mechanisms that control the high-latitude asymmetry in flux amplification found in this study should be an important goal for mechanistic land surface models moving forward.

Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle.

Carbon fixation via the Calvin cycle is constrained by the side activity of Rubisco with dioxygen, generating 2-phosphoglycolate. The metabolic recycling of phosphoglycolate was extensively studied in photoautotrophic organisms, including plants, algae, and cyanobacteria, where it is referred to as photorespiration. While receiving little attention so far, aerobic chemolithoautotrophic bacteria that operate the Calvin cycle independent of light must also recycle phosphoglycolate. As the term photorespiration is inappropriate for describing phosphoglycolate recycling in these nonphotosynthetic autotrophs, we suggest the more general term "phosphoglycolate salvage." Here, we study phosphoglycolate salvage in the model chemolithoautotroph Cupriavidus necator H16 (Ralstonia eutropha H16) by characterizing the proxy process of glycolate metabolism, performing comparative transcriptomics of autotrophic growth under low and high CO2 concentrations, and testing autotrophic growth phenotypes of gene deletion strains at ambient CO2 We find that the canonical plant-like C2 cycle does not operate in this bacterium, and instead, the bacterial-like glycerate pathway is the main route for phosphoglycolate salvage. Upon disruption of the glycerate pathway, we find that an oxidative pathway, which we term the malate cycle, supports phosphoglycolate salvage. In this cycle, glyoxylate is condensed with acetyl coenzyme A (acetyl-CoA) to give malate, which undergoes two oxidative decarboxylation steps to regenerate acetyl-CoA. When both pathways are disrupted, autotrophic growth is abolished at ambient CO2 We present bioinformatic data suggesting that the malate cycle may support phosphoglycolate salvage in diverse chemolithoautotrophic bacteria. This study thus demonstrates a so far unknown phosphoglycolate salvage pathway, highlighting important diversity in microbial carbon fixation metabolism.

Large and projected strengthening moisture limitation on end-of-season photosynthesis.

Terrestrial photosynthesis is regulated by plant phenology and environmental conditions, both of which experienced substantial changes in recent decades. Unlike early-season photosynthesis, which is mostly driven by temperature or wet-season onset, late-season photosynthesis can be limited by several factors and the underlying mechanisms are less understood. Here, we analyze the temperature and water limitations on the ending date of photosynthesis (EOP), using data from both remote-sensing and flux tower-based measurements. We find a contrasting spatial pattern of temperature and water limitations on EOP. The threshold separating these is determined by the balance between energy availability and soil water supply. This coordinated temperature and moisture regulation can be explained by "law of minimum," i.e., as temperature limitation diminishes, higher soil water is needed to support increased vegetation activity, especially during the late growing season. Models project future warming and drying, especially during late season, both of which should further expand the water-limited regions, causing large variations and potential decreases in photosynthesis.

The origin and diversification of pteropods precede past perturbations in the Earth's carbon cycle.

Pteropods are a group of planktonic gastropods that are widely regarded as biological indicators for assessing the impacts of ocean acidification. Their aragonitic shells are highly sensitive to acute changes in ocean chemistry. However, to gain insight into their potential to adapt to current climate change, we need to accurately reconstruct their evolutionary history and assess their responses to past changes in the Earth's carbon cycle. Here, we resolve the phylogeny and timing of pteropod evolution with a phylogenomic dataset (2,654 genes) incorporating new data for 21 pteropod species and revised fossil evidence. In agreement with traditional taxonomy, we recovered molecular support for a division between "sea butterflies" (Thecosomata; mucus-web feeders) and "sea angels" (Gymnosomata; active predators). Molecular dating demonstrated that these two lineages diverged in the early Cretaceous, and that all main pteropod clades, including shelled, partially-shelled, and unshelled groups, diverged in the mid- to late Cretaceous. Hence, these clades originated prior to and subsequently survived major global change events, including the Paleocene-Eocene Thermal Maximum (PETM), the closest analog to modern-day ocean acidification and warming. Our findings indicate that planktonic aragonitic calcifiers have shown resilience to perturbations in the Earth's carbon cycle over evolutionary timescales.

The McdAB system positions α-carboxysomes in proteobacteria.

Carboxysomes are protein-based organelles essential for carbon fixation in cyanobacteria and proteobacteria. Previously, we showed that the cyanobacterial nucleoid is used to equally space out ß-carboxysomes across cell lengths by a two-component system (McdAB) in the model cyanobacterium Synechococcus elongatus PCC 7942. More recently, we found that McdAB systems are widespread among ß-cyanobacteria, which possess ß-carboxysomes, but are absent in α-cyanobacteria, which possess structurally and phyletically distinct α-carboxysomes. Cyanobacterial α-carboxysomes are thought to have arisen in proteobacteria and then horizontally transferred into cyanobacteria, which suggests that α-carboxysomes in proteobacteria may also lack the McdAB system. Here, using the model chemoautotrophic proteobacterium Halothiobacillus neapolitanus, we show that a McdAB system distinct from that of ß-cyanobacteria operates to position α-carboxysomes across cell lengths. We further show that this system is widespread among α-carboxysome-containing proteobacteria and that cyanobacteria likely inherited an α-carboxysome operon from a proteobacterium lacking the mcdAB locus. These results demonstrate that McdAB is a cross-phylum two-component system necessary for positioning both α- and ß-carboxysomes. The findings have further implications for understanding the positioning of other protein-based bacterial organelles involved in diverse metabolic processes. PLAIN LANGUAGE SUMMARY: Cyanobacteria are well known to fix atmospheric CO2 into sugars using the enzyme Rubisco. Less appreciated are the carbon-fixing abilities of proteobacteria with diverse metabolisms. Bacterial Rubisco is housed within organelles called carboxysomes that increase enzymatic efficiency. Here we show that proteobacterial carboxysomes are distributed in the cell by two proteins, McdA and McdB. McdA on the nucleoid interacts with McdB on carboxysomes to equidistantly space carboxysomes from one another, ensuring metabolic homeostasis and a proper inheritance of carboxysomes following cell division. This study illuminates how widespread carboxysome positioning systems are among diverse bacteria. Carboxysomes significantly contribute to global carbon fixation; therefore, understanding the spatial organization mechanism shared across the bacterial world is of great interest.

Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean.

Sinking particles are a critical conduit for the export of organic material from surface waters to the deep ocean. Despite their importance in oceanic carbon cycling and export, little is known about the biotic composition, origins, and variability of sinking particles reaching abyssal depths. Here, we analyzed particle-associated nucleic acids captured and preserved in sediment traps at 4,000-m depth in the North Pacific Subtropical Gyre. Over the 9-month time-series, Bacteria dominated both the rRNA-gene and rRNA pools, followed by eukaryotes (protists and animals) and trace amounts of Archaea. Deep-sea piezophile-like Gammaproteobacteria, along with Epsilonproteobacteria, comprised >80% of the bacterial inventory. Protists (mostly Rhizaria, Syndinales, and ciliates) and metazoa (predominantly pelagic mollusks and cnidarians) were the most common sinking particle-associated eukaryotes. Some near-surface water-derived eukaryotes, especially Foraminifera, Radiolaria, and pteropods, varied greatly in their abundance patterns, presumably due to sporadic export events. The dominance of piezophile-like Gammaproteobacteria and Epsilonproteobacteria, along with the prevalence of their nitrogen cycling-associated gene transcripts, suggested a central role for these bacteria in the mineralization and biogeochemical transformation of sinking particulate organic matter in the deep ocean. Our data also reflected several different modes of particle export dynamics, including summer export, more stochastic inputs from the upper water column by protists and pteropods, and contributions from sinking mid- and deep-water organisms. In total, our observations revealed the variable and heterogeneous biological origins and microbial activities of sinking particles that connect their downward transport, transformation, and degradation to deep-sea biogeochemical processes.

Mechanistic evidence for tracking the seasonality of photosynthesis with solar-induced fluorescence.

Northern hemisphere evergreen forests assimilate a significant fraction of global atmospheric CO2 but monitoring large-scale changes in gross primary production (GPP) in these systems is challenging. Recent advances in remote sensing allow the detection of solar-induced chlorophyll fluorescence (SIF) emission from vegetation, which has been empirically linked to GPP at large spatial scales. This is particularly important in evergreen forests, where traditional remote-sensing techniques and terrestrial biosphere models fail to reproduce the seasonality of GPP. Here, we examined the mechanistic relationship between SIF retrieved from a canopy spectrometer system and GPP at a winter-dormant conifer forest, which has little seasonal variation in canopy structure, needle chlorophyll content, and absorbed light. Both SIF and GPP track each other in a consistent, dynamic fashion in response to environmental conditions. SIF and GPP are well correlated (R2 = 0.62-0.92) with an invariant slope over hourly to weekly timescales. Large seasonal variations in SIF yield capture changes in photoprotective pigments and photosystem II operating efficiency associated with winter acclimation, highlighting its unique ability to precisely track the seasonality of photosynthesis. Our results underscore the potential of new satellite-based SIF products (TROPOMI, OCO-2) as proxies for the timing and magnitude of GPP in evergreen forests at an unprecedented spatiotemporal resolution.

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil.

Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was Narnaviridae that may parasitize fungi or Leviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.

Hybrid Cyanobacterial-Tobacco Rubisco Supports Autotrophic Growth and Procarboxysomal Aggregation.

Much of the research aimed at improving photosynthesis and crop productivity attempts to overcome shortcomings of the primary CO2-fixing enzyme Rubisco. Cyanobacteria utilize a CO2-concentrating mechanism (CCM), which encapsulates Rubisco with poor specificity but a relatively fast catalytic rate within a carboxysome microcompartment. Alongside the active transport of bicarbonate into the cell and localization of carbonic anhydrase within the carboxysome shell with Rubisco, cyanobacteria are able to overcome the limitations of Rubisco via localization within a high-CO2 environment. As part of ongoing efforts to engineer a ß-cyanobacterial CCM into land plants, we investigated the potential for Rubisco large subunits (LSU) from the ß-cyanobacterium Synechococcus elongatus (Se) to form aggregated Rubisco complexes with the carboxysome linker protein CcmM35 within tobacco (Nicotiana tabacum) chloroplasts. Transplastomic plants were produced that lacked cognate Se Rubisco small subunits (SSU) and expressed the Se LSU in place of tobacco LSU, with and without CcmM35. Plants were able to form a hybrid enzyme utilizing tobacco SSU and the Se LSU, allowing slow autotrophic growth in high CO2 CcmM35 was able to form large Rubisco aggregates with the Se LSU, and these incorporated small amounts of native tobacco SSU. Plants lacking the Se SSU showed delayed growth, poor photosynthetic capacity, and significantly reduced Rubisco activity compared with both wild-type tobacco and lines expressing the Se SSU. These results demonstrate the ability of the Se LSU and CcmM35 to form large aggregates without the cognate Se SSU in planta, harboring active Rubisco that enables plant growth, albeit at a much slower pace than plants expressing the cognate Se SSU.