Dark CO2 Fixation Research Articles

Organic manure rather than chemical fertilization improved dark CO2 fixation by regulating associated microbial functional traits in upland red soils

Dark microbial fixation of CO2 is an indispensable process for soil carbon sequestration. However, the whole genetic information involved in dark CO2 fixation and its influence on dark CO2 fixation rates under diversified fertilization regimes were largely unclear. Here, revealed by 13C-CO2 labeling, dark CO2 fixation rates in upland red soils ranged from 0.029 mg kg−1 d−1 to 0.092 mg kg−1 d−1, and it was 75.49 % higher (P < 0.05) in organic manure (OM) soil but 44.2 % decline (P < 0.05) in chemical nitrogen fertilizer (N) soil compared to unfertilized (CK) soil. In addition, the normalized abundance and Chao1 index of dark CO2 fixation genes (KO level) were significantly different between OM and N soils, showing the highest and lowest, respectively. And they were positively (P < 0.05) correlated with dark CO2 fixation rate. Besides, among the identified CO2 fixation pathways in this study, the DC/4-HB cycle (M00374) was enriched in OM soil, yet the 3-HP cycle (M00376) was enriched in N soil, and their relative abundances were positively and negatively correlated (P < 0.05) with dark CO2 fixation rate, respectively. The PLS-SEM analysis revealed that dark CO2 fixation-related functional traits (i.e. normalized abundance, Chao1 index and gene composition) were directly and positively associated with dark CO2 fixation rate, and organic manure could exert a positive effect on soil dark CO2 fixation rate through enhancing soil properties (e.g., pH and soil organic carbon) and further altering associated microbial functional traits. These results have implications for explaining and predicting the soil CO2 fixation process from the perspective of microbial functional potential.

Wood-Ljungdahl pathway encoding anaerobes facilitate low-cost primary production in hypersaline sediments at Great Salt Lake, Utah.

Little is known of primary production in dark hypersaline ecosystems despite the prevalence of such environments on Earth today and throughout its geologic history. Here, we generated and analyzed metagenome-assembled genomes (MAGs) organized as operational taxonomic units (OTUs) from three depth intervals along a 30-cm sediment core from the north arm of Great Salt Lake, Utah. The sediments and associated porewaters were saturated with NaCl, exhibited redox gradients with depth, and harbored nitrogen-depleted organic carbon. Metabolic predictions of MAGs representing 36 total OTUs recovered from the core indicated that communities transitioned from aerobic and heterotrophic at the surface to anaerobic and autotrophic at depth. Dark CO2 fixation was detected in sediments and the primary mode of autotrophy was predicted to be via the Wood-Ljungdahl pathway. This included novel hydrogenotrophic acetogens affiliated with the bacterial class Candidatus Bipolaricaulia. Minor populations were dependent on the Calvin cycle and the reverse tricarboxylic acid cycle, including in a novel Thermoplasmatota MAG. These results are interpreted to reflect the favorability of and selectability for populations that operate the lowest energy requiring CO2-fixation pathway known, the Wood-Ljungdahl pathway, in anoxic and hypersaline conditions that together impart a higher energy demand on cells.

Bacterioplankton dark CO2 fixation in oligotrophic waters

Abstract. Dark CO2 fixation by bacteria is believed to be particularly important in oligotrophic ecosystems. However, only a few studies have characterized the role of bacterial dissolved inorganic carbon (DIC) fixation in global carbon dynamics. Therefore, this study quantified the primary production (PP), total bacteria dark CO2 fixation (TBDIC fixation), and heterotrophic bacterial production (HBP) in the warm and oligotrophic Red Sea using stable-isotope labeling and cavity ring-down spectroscopy (13C–CRDS). Additionally, we assessed the contribution of bacterial DIC fixation (TBDIC %) relative to the total DIC fixation (totalDIC fixation). Our study demonstrated that TBDIC fixation increased the totalDIC fixation from 2.03 to 60.45 µg C L−1 d−1 within the photic zone, contributing 13.18 % to 71.68 % with an average value of 33.95 ± 0.02 % of the photic layer totalDIC fixation. The highest TBDIC fixation values were measured at the surface and deep (400 m) water with an average value of 5.23 ± 0.45 and 4.95 ± 1.33 µg C L−1 d−1, respectively. These findings suggest that the non-photosynthetic processes such as anaplerotic DIC reactions and chemoautotrophic CO2 fixation extended to the entire oxygenated water column. On the other hand, the percent of TBDIC contribution to totalDIC fixation increased as primary production decreased (R2=0.45, p&lt;0.0001), suggesting the relevance of increased dark DIC fixation when photosynthetic production was low or absent, as observed in other systems. Therefore, when estimating the total carbon dioxide production in the ocean, dark DIC fixation must also be accounted for as a crucial component of the carbon dioxide flux in addition to photosynthesis.

Sources of carbon supporting the fast growth of developing immature moso bamboo (Phyllostachys edulis) culms: inference from carbon isotopes and anatomy.

Phyllostachys edulis is a spectacularly fast-growing species that completes its height growth within 2 months after the shoot emerges without producing leaves (fast-growing period, FGP). This phase was considered heterotrophic, with the carbon necessary for the growth being transferred from the mature culms via the rhizomes, although previous studies observed key enzymes and anatomical features related to C4-carbon fixation in developing culms. We tested whether C4-photosynthesis or dark-CO2 fixation through anaplerotic reactions significantly contributes to the FGP, resulting in differences in the natural abundance of δ13C in bulk organic matter and organic compounds. Further, pulse-13CO2-labelling was performed on developing culms, either from the surface or from the internal hollow, to ascertain whether significant CO2 fixation occurs in developing culms. δ13C of young shoots and developing culms were higher (-26.3 to -26.9 ‰) compared to all organs of mature bamboos (-28.4 to -30.1 ‰). Developing culms contained chlorophylls, most observed in the skin tissues. After pulse-13CO2-labelling, the polar fraction extracted from the skin tissues was slightly enriched in 13C, and only a weak 13C enrichment was observed in inner tissues. Main carbon source sustaining the FGP was not assimilated by the developing culm, while a limited anaplerotic fixation of respired CO2 cannot be excluded and is more likely than C4-photosynthetic carbon fixation.

Distribution, Size-Morphological Structure and Production of Heterotrophic Bacterioplankton in Gorky Reservoir

The abundance, biomass, size-morphological structure, growth rate and production of bacterioplankton, the intensity of primary phytoplankton production and dark fixation of CO2, as well as the abundance and biomass of heterotrophic nanoflagellates were determined in a large plain eutrophic reservoir (Gorky Reservoir, Middle Volga). The abundance, biomass, and production of bacterioplankton were relatively high and averaged 7.6 × 106 cells/mL, 117.9 mg C/m3, and 59.2 mg C/(m3 × day), respectively. Heterotrophic nanoflagellates reached a high level of quantitative development – 6.9 × 103 cells/mL, 47.9 mg C/m3. Their biomass averaged 41.6 ± 18.4% of the bacterioplankton biomass, which indicates that, in addition to bacteria, nanoflagellates used other food sources. Small rods and cocci dominated among the size-morphological bacterioplankton groups and accounted for 36.3 and 33.3% of its total abundance, respectively. Small rods averaged more than a half (56.2%) of the total biomass and were the most stable component of the community. The growth rate and production of bacterioplankton increased in those parts of the reservoir where the medium-sized cocci and coccobacilli accounted for from 18.2 to 29.3% of the total abundance. The highest bacterial activity was recorded in the area affected by the warm waste waters of the Volgorechensk State District Power Plant. Based on the data obtained, the reservoir divided on the upper river section and the lower lake section.

Anoxia-Related Biogeochemistry of North Indian Ocean

Complex interactions between microbial communities and geochemical processes drive the major element cycles and control the function of marine sediments as a dynamic reservoir of organic matter. Sulfate reduction is globally the dominant pathway of anaerobic mineralisation and is the main source of sulfide. The effective re-oxidation of this sulfide at the direct or indirect expense of oxygen is a prerequisite for aerobic life on our planet. Although largely hidden beneath the oxic sediment surface, the sulfur cycle is therefore critical for Earth’s redox state. This Geochemical Perspectives begins with a brief primer on the sulfur cycle of marine sediments and a description of my own scientific journey through nearly fifty years of studies of sulfur geochemistry and microbiology. Among the main objectives of these studies were to quantify the main processes of the sulfur cycle and to identify the microbial communities behind them. Radiotracers in combination with chemical analyses have thereby been used extensively for laboratory experiments, supported by diverse molecular microbiological methods. The following sections discuss the main processes of sulfate reduction, sulfide oxidation and disproportionation of the inorganic sulfur intermediates, especially of elemental sulfur and thiosulfate. The experimental approaches used enable the analysis of how environmental factors such as substrate concentration or temperature affect process rates and how concurrent processes of sulfate reduction and sulfide oxidation drive a cryptic sulfur cycle. The chemical energy of sulfide is used by chemolithotrophic bacteria, including fascinating communities of big sulfur bacteria and cable bacteria, and supports their dark CO2 fixation, which produces new microbial biomass. During the burial and aging of marine sediments, the predominant mineralisation processes change through a cascade of redox reactions, and the rate of organic matter degradation drops continuously over many orders of magnitude. The main pathways of anaerobic mineralisation and the age control of the organic matter turnover are discussed. In the deep methanic zone, only a few percent of the entire degradation process remains, which provides a small boost of substrate for sulfate reduction through the process of anaerobic methane oxidation. The stable isotopes of sulfur provide an additional tool to understand these diagenetic processes, whereby the combination of microbial isotope fractionation and open system diagenesis generate a differential diffusion flux of the isotopes. In relation to the organic carbon cycle of the seabed and the contribution of methane, the paper discusses the global sulfur budget and the role of sulfate reduction for organic matter mineralisation in different depth regions of the ocean - from coast to deep sea. The published estimates of these parameters are evaluated and compared. Finally, the paper looks at future perspectives with respect to gaps in our current understanding and the need for further studies.

Temperature sensitivity of dark CO2 fixation in temperate forest soils

Abstract. Globally, soil temperature to 1 m depth is predicted to be up to 4 ∘C warmer by the end of this century, with pronounced effects expected in temperate forest regions. Increased soil temperatures will potentially increase the release of carbon dioxide (CO2) from temperate forest soils, resulting in important positive feedback on climate change. Dark CO2 fixation by microbes can recycle some of the released soil CO2, and CO2 fixation rates are reported to increase under higher temperatures. However, research on the influence of temperature on dark CO2 fixation rates, particularly in comparison to the temperature sensitivity of respiration in soils of temperate forest regions, is missing. To determine the temperature sensitivity (Q10) of dark CO2 fixation and respiration rates, we investigated soil profiles to 1 m depth from beech (deciduous) and spruce (coniferous) forest plots of the Hummelshain forest, Germany. We used 13C-CO2 labelling and incubations of soils at 4 and 14 ∘C to determine CO2 fixation and net soil respiration rates and derived the Q10 values for both processes with depth. The average Q10 for dark CO2 fixation rates normalized to soil dry weight was 2.07 for beech and spruce profiles, and this was lower than the measured average Q10 of net soil respiration rates with ∼2.98. Assuming these Q10 values, we extrapolated that net soil respiration might increase 1.16 times more than CO2 fixation under a projected 4 ∘C warming. In the beech soil, a proportionally larger fraction of the label CO2 was fixed into soil organic carbon than into microbial biomass compared to the spruce soil. This suggests a primarily higher rate of microbial residue formation (i.e. turnover as necromass or release of extracellular products). Despite a similar abundance of the total bacterial community in the beech and spruce soils, the beech soil also had a lower abundance of autotrophs, implying a higher proportion of heterotrophs when compared to the spruce soil; hence this might partly explain the higher rate of microbial residue formation in the beech soil. Furthermore, higher temperatures in general lead to higher microbial residues formed in both soils. Our findings suggest that in temperate forest soils, CO2 fixation might be less responsive to future warming than net soil respiration and could likely recycle less CO2 respired from temperate forest soils in the future than it does now.

Dark CO2 fixation in temperate beech and pine forest soils

Soils are the largest terrestrial organic carbon pool and the largest terrestrial source of atmospheric CO2. Non-phototrophic CO2 fixation by microbes re-fixes and recycles CO2 respired in soils. Our previous study showed that in temperate deciduous forest soil profiles, rates of dark CO2 fixation were proportional to microbial biomass, irrespective of soil depth. However, the amount and quality of organic matter entering different soil depths vary for different temperate forest types and these influence microbial communities with unknown consequences for CO2 fixation rates. To test whether differences in the amount and quality of SOC caused by tree species affect dark CO2 fixation rates with depth, we conducted a study using acidic soils from two forest plots from the Schorfheide-Chorin Exploratory, Germany. These soils, dominated by either beech (deciduous) or pine (coniferous) tree stands differ in their SOC content and quality. We traced the incorporation of 2% (v:v) 13C–CO2 label into microbial biomass and estimated the CO2 fixation rates relative to microbial biomass carbon content (in μg C g MBC−1 d−1) across the soil profiles. The rates of dark CO2 fixation per g MBC were similar across the beech soil profiles, but significantly lower in the pine soils at the B2 and BC horizons, suggesting that while dark CO2 fixation rates are linked to MBC in deciduous forest soils, other factors influence dark CO2 fixation rates in coniferous forest soils. The pine subsoils had low SOC content and quality, with a microbial community enriched with heterotrophic fermenters like Chloroflexi that are predicted to have a lower potential for heterotrophic CO2 fixation compared to the other dominant bacteria phyla. In contrast, the beech soil profiles, characterized by higher SOC inputs, featured higher fractions of copiotrophs like Proteobacteria, Acidobacteria, and Actinobacteria predicted to have high heterotrophic CO2 fixation potential. We thus speculate that in contrast to the beech soils, lower SOC inputs in the pine subsoils affected the community composition, leading to lower CO2 fixation rates. We further made comparisons to soils dominated by mixed deciduous trees and featuring a higher MBC and SOC content. Over this range of temperate forest soils, CO2 fixation rates were highest in the mixed deciduous forest soils, with MBC and Shannon index (used as a proxy parameter for community composition) showing the strongest correlations with the varying CO2 fixation rates. Our study suggests that predictions of dark CO2 fixation rates need to consider tree-species specific or site-specific conditions, as these may alter root carbon inputs and affect microbial community composition and their metabolic CO2 fixation potentials in soil.

Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater

Current understanding of organic carbon inputs into ecosystems lacking photosynthetic primary production is predicated on data and inferences derived almost entirely from metagenomic analyses. The elevated abundances of putative chemolithoautotrophs in groundwaters suggest that dark CO2 fixation is an integral component of subsurface trophic webs. To understand the impact of autotrophically fixed carbon, the flux of CO2-derived carbon through various populations of subsurface microbiota must first be resolved, both quantitatively and temporally. Here we implement novel Stable Isotope Cluster Analysis to render a time-resolved and quantitative evaluation of 13CO2-derived carbon flow through a groundwater community in microcosms stimulated with reduced sulfur compounds. We demonstrate that mixotrophs, not strict autotrophs, were the most abundant active organisms in groundwater microcosms. Species of Hydrogenophaga, Polaromonas, Dechloromonas, and other metabolically versatile mixotrophs drove the production and remineralization of organic carbon. Their activity facilitated the replacement of 43% and 80% of total microbial carbon stores in the groundwater microcosms with 13C in just 21 and 70 days, respectively. The mixotrophs employed different strategies for satisfying their carbon requirements by balancing CO2 fixation and uptake of available organic compounds. These different strategies might provide fitness under nutrient-limited conditions, explaining the great abundances of mixotrophs in other oligotrophic habitats, such as the upper ocean and boreal lakes.

CAM photosynthesis: the acid test.

SummaryThere is currently considerable interest in the prospects for bioengineering crassulacean acid metabolism (CAM) photosynthesis – or key elements associated with it, such as increased water‐use efficiency – into C3 plants. Resolving how CAM photosynthesis evolved from the ancestral C3 pathway could provide valuable insights into the targets for such bioengineering efforts. It has been proposed that the ability to accumulate organic acids at night may be common among C3 plants, and that the transition to CAM might simply require enhancement of pre‐existing fluxes, without the need for changes in circadian or diurnal regulation. We show, in a survey encompassing 40 families of vascular plants, that nocturnal acidification is a feature entirely restricted to CAM species. Although many C3 species can synthesize malate during the light period, we argue that the switch to night‐time malic acid accumulation requires a fundamental metabolic reprogramming that couples glycolytic breakdown of storage carbohydrate to the process of net dark CO2 fixation. This central element of the CAM pathway, even when expressed at a low level, represents a biochemical capability not seen in C3 plants, and so is better regarded as a discrete evolutionary innovation than as part of a metabolic continuum between C3 and CAM.

Sulfur Biogeochemical Cycle of Marine Sediments

Complex interactions between microbial communities and geochemical processes drive the major element cycles and control the function of marine sediments as a dynamic reservoir of organic matter. Sulfate reduction is globally the dominant pathway of anaerobic mineralisation and is the main source of sulfide. The effective re-oxidation of this sulfide at the direct or indirect expense of oxygen is a prerequisite for aerobic life on our planet. Although largely hidden beneath the oxic sediment surface, the sulfur cycle is therefore critical for Earth’s redox state. This Geochemical Perspectives begins with a brief primer on the sulfur cycle of marine sediments and a description of my own scientific journey through nearly fifty years of studies of sulfur geochemistry and microbiology. Among the main objectives of these studies were to quantify the main processes of the sulfur cycle and to identify the microbial communities behind them. Radiotracers in combination with chemical analyses have thereby been used extensively for laboratory experiments, supported by diverse molecular microbiological methods. The following sections discuss the main processes of sulfate reduction, sulfide oxidation and disproportionation of the inorganic sulfur intermediates, especially of elemental sulfur and thiosulfate. The experimental approaches used enable the analysis of how environmental factors such as substrate concentration or temperature affect process rates and how concurrent processes of sulfate reduction and sulfide oxidation drive a cryptic sulfur cycle. The chemical energy of sulfide is used by chemolithotrophic bacteria, including fascinating communities of big sulfur bacteria and cable bacteria, and supports their dark CO2 fixation, which produces new microbial biomass. During the burial and aging of marine sediments, the predominant mineralisation processes change through a cascade of redox reactions, and the rate of organic matter degradation drops continuously over many orders of magnitude. The main pathways of anaerobic mineralisation and the age control of the organic matter turnover are discussed. In the deep methanic zone, only a few percent of the entire degradation process remains, which provides a small boost of substrate for sulfate reduction through the process of anaerobic methane oxidation. The stable isotopes of sulfur provide an additional tool to understand these diagenetic processes, whereby the combination of microbial isotope fractionation and open system diagenesis generate a differential diffusion flux of the isotopes. In relation to the organic carbon cycle of the seabed and the contribution of methane, the paper discusses the global sulfur budget and the role of sulfate reduction for organic matter mineralisation in different depth regions of the ocean – from coast to deep sea. The published estimates of these parameters are evaluated and compared. Finally, the paper looks at future perspectives with respect to gaps in our current understanding and the need for further studies.

Rates of dark CO2 fixation are driven by microbial biomass in a temperate forest soil

Soils substantially contribute to the terrestrial fluxes of CO2 to the atmosphere. Dark CO2 fixation, the microbial process by which pore space CO2 is reduced to organic matter, may recycle and trap some of the CO2 respired in soils before it can escape to the atmosphere. To evaluate its potential significance for global temperate forest soil carbon stocks, we quantified dark CO2 fixation rates in a temperate beech forest soil down to 1 m depth over a range of 2–20% (v:v) headspace CO2 concentrations, by tracing incorporation of a13C–CO2 label into microbial biomass carbon and soil organic matter. We found that fixation rates under a concentration of 2% CO2 decreased with depth from 0.86 to 0.06 μg C normalized to g(dw) soil−1 d−1. However, when dark CO2 fixation rates were normalized to soil microbial biomass carbon, no significant differences between depths were observed. Higher CO2 concentrations increased fixation rates, with a linear 2-fold increase between 2% and 10% CO2. Molecular analysis revealed the dominance of heterotrophs, along with the presence of autotrophs mainly employing the Calvin Benson Bassham (CBB) pathway followed by the reductive citric acid (rTCA) pathway. Although community composition varied with depth, the relative fraction of autotrophs determined by qPCR of RuBisCO (cbbL IA, cbbL IC) and ATP-citrate lyase (aclA) genes remained stable at approximately 0.5% of the total community. Dark CO2 fixed carbon accounted for up to 1.1% of microbial biomass carbon and up to 0.035% of soil organic carbon after 28 days. We estimated a fixation flux of 25 ± 7.2 g C m−2 yr−1 to 1 m depth for the Hainich forest soil under field conditions. Without this process, Hainich forest soil CO2 emissions would be 5.6% higher, recycling a fraction of carbon large enough to potentially affect carbon isotope signatures in SOC. If this is held for all temperate forest soils globally, the annual rate of dark CO2 fixation would be 0.26 ± 0.07 Pg C yr−1 to a depth of 1 m, without considering contributions from other biomes. In conclusion, microbial biomass carbon and CO2 concentration appear to be the main drivers of dark CO2 fixation in temperate forest soils, and dark CO2 fixation may maintain Hainich forest soil carbon stocks by moderating a significant fraction of soil CO2 emissions annually.

Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism.

BackgroundCrassulacean acid metabolism (CAM), a specialized mode of photosynthesis, enables plant adaptation to water-limited environments and improves photosynthetic efficiency via an inorganic carbon-concentrating mechanism. Kalanchoë fedtschenkoi is an obligate CAM model featuring a relatively small genome and easy stable transformation. However, the molecular responses to light quality and intensity in CAM plants remain understudied.ResultsHere we present a genome-wide expression atlas of K. fedtschenkoi plants grown under 12 h/12 h photoperiod with different light quality (blue, red, far-red, white light) and intensity (0, 150, 440, and 1,000 μmol m–2 s–1) based on RNA sequencing performed for mature leaf samples collected at dawn (2 h before the light period) and dusk (2 h before the dark period). An eFP web browser was created for easy access of the gene expression data. Based on the expression atlas, we constructed a light-responsive co-expression network to reveal the potential regulatory relationships in K. fedtschenkoi. Measurements of leaf titratable acidity, soluble sugar, and starch turnover provided metabolic indicators of the magnitude of CAM under the different light treatments and were used to provide biological context for the expression dataset. Furthermore, CAM-related subnetworks were highlighted to showcase genes relevant to CAM pathway, circadian clock, and stomatal movement. In comparison with white light, monochrome blue/red/far-red light treatments repressed the expression of several CAM-related genes at dusk, along with a major reduction in acid accumulation. Increasing light intensity from an intermediate level (440 μmol m−2 s−1) of white light to a high light treatment (1,000 μmol m–2 s–1) increased expression of several genes involved in dark CO2 fixation and malate transport at dawn, along with an increase in organic acid accumulation.ConclusionsThis study provides a useful genomics resource for investigating the molecular mechanism underlying the light regulation of physiology and metabolism in CAM plants. Our results support the hypothesis that both light intensity and light quality can modulate the CAM pathway through regulation of CAM-related genes in K. fedtschenkoi.

Kalanchoë PPC1 Is Essential for Crassulacean Acid Metabolism and the Regulation of Core Circadian Clock and Guard Cell Signaling Genes.

Unlike C3 plants, Crassulacean acid metabolism (CAM) plants fix CO2 in the dark using phosphoenolpyruvate carboxylase (PPC; EC 4.1.1.31). PPC combines phosphoenolpyruvate with CO2 (as HCO3 -), forming oxaloacetate. The oxaloacetate is converted to malate, leading to malic acid accumulation in the vacuole, which peaks at dawn. During the light period, malate decarboxylation concentrates CO2 around Rubisco for secondary fixation. CAM mutants lacking PPC have not been described. Here, we employed RNA interference to silence the CAM isogene PPC1 in Kalanchoë laxiflora Line rPPC1-B lacked PPC1 transcripts, PPC activity, dark period CO2 fixation, and nocturnal malate accumulation. Light period stomatal closure was also perturbed, and the plants displayed reduced but detectable dark period stomatal conductance and arrhythmia of the CAM CO2 fixation circadian rhythm under constant light and temperature free-running conditions. By contrast, the rhythm of delayed fluorescence was enhanced in plants lacking PPC1 Furthermore, a subset of gene transcripts within the central circadian oscillator was upregulated and oscillated robustly in this line. The regulation of guard cell genes involved in controlling stomatal movements was also perturbed in rPPC1-B These findings provide direct evidence that the regulatory patterns of key guard cell signaling genes are linked with the characteristic inverse pattern of stomatal opening and closing during CAM.

Dark CO2 fixation into phospholipid-derived fatty acids by the cold-water coral associated sponge Hymedesmia (Stylopus) coriacea (Tisler Reef, NE Skagerrak)

ABSTRACTMany cold-water sponges harbour microorganisms of which the role in the sponge host remains enigmatic. Here, we show a transfer of fixed inorganic carbon by sponge-associated microbes to its host, the cold-water coral encrusting sponge Hymedesmia (Stylopus) coriacea. Sponge were collected at approx. 100 m depth and incubated for 1.5–2.5 days with 13C labelled dissolved inorganic carbon (DIC) as tracer. Total DIC fixation rates ranged from 0.03–0.11 mmol C × mmol Csponge × d−1. 13C-tracer was recovered in bacterial-specific (i.e. short and branched) and sponge-specific (very long-chained) phospholipid-derived fatty acids (PLFA's), but was not incorporated into archaeal lipids. 13C-incorporation in biomarkers such as C16:1w7c and C18:1w7c indicated that nitrifying and/or sulphur-oxidizing bacteria (chemoautotrophs) were likely active in the sponge. Trophic transfer of microbially-fixed carbon to the sponge host was confirmed by recovery of label in very long chain fatty acids (VLCFA's) including C26:2 and C26:3. Tracer accumulation into several VLCFA's continued after removal of 13C-DIC, while tracer in most bacteria-specific PLFA's declined, indicating a transfer and elongation of bacterial-specific PLFA's to sponge-specific PLFA's. This implies that PLFA precursors released from chemo- as well as heterotrophic microbes in sponges contributed to the synthesis of VLCFA's, identifying sponge-associated bacteria as symbionts of the sponge.

Blue carbon sequestration dynamics within tropical seagrass sediments: long-term incubations for changes over climatic scales

Determination of blue carbon sequestration in seagrass sediments over climatic time scales (&amp;gt;100 years) relies on several assumptions, including no loss of particulate organic carbon (POC) after 1–2 years, tight coupling between POC loss and CO2 emissions, no dissolution of carbonates, and removal of the recalcitrant black carbon (BC) contribution. We tested these assumptions via 500-day anoxic decomposition and mineralisation experiments to capture centennial parameter decay dynamics from two sediment horizons robustly dated as 2 and 18 years old. No loss of BC was detected, and decay of POC was best described for both horizons by near-identical reactivity continuum models. The models predicted average losses of 49 and 51% after 100 years of burial for the surface and 20–22-cm horizons respectively. However, the loss rate of POC was far greater than the release rate of CO2, even after accounting for CO2 from particulate inorganic carbon (PIC) production, possibly as siderite. The deficit could not be attributed to dissolved organic carbon or dark CO2 fixation. Instead, evidence based on δ13CO2, acidity and lack of sulfate reduction suggested methanogenesis. The results indicated the importance of centennial losses of POC and PIC precipitation and possibly methanogenesis in estimating carbon sequestration rates.

Dark microbial CO2 fixation in temperate forest soils increases with CO2 concentration.

Dark, that is, nonphototrophic, microbial CO2 fixation occurs in a large range of soils. However, it is still not known whether dark microbial CO2 fixation substantially contributes to the C balance of soils and what factors control this process. Therefore, the objective of this study was to quantitate dark microbial CO2 fixation in temperate forest soils, to determine the relationship between the soil CO2 concentration and dark microbial CO2 fixation, and to estimate the relative contribution of different microbial groups to dark CO2 fixation. For this purpose, we conducted a 13 C-CO2 labeling experiment. We found that the rates of dark microbial CO2 fixation were positively correlated with the CO2 concentration in all soils. Dark microbial CO2 fixation amounted to up to 320µgCkg-1 soilday-1 in the Ah horizon. The fixation rates were 2.8-8.9 times higher in the Ah horizon than in the Bw1 horizon. Although the rates of dark microbial fixation were small compared to the respiration rate (1.2%-3.9% of the respiration rate), our findings suggest that organic matter formed by microorganisms from CO2 contributes to the soil organic matter pool, especially given that microbial detritus is more stable in soil than plant detritus. Phospholipid fatty acid analyses indicated that CO2 was mostly fixed by gram-positive bacteria, and not by fungi. In conclusion, our study shows that the dark microbial CO2 fixation rate in temperate forest soils increases in periods of high CO2 concentrations, that dark microbial CO2 fixation is mostly accomplished by gram-positive bacteria, and that dark microbial CO2 fixation contributes to the formation of soil organic matter.

Relevance of Nutrient-Limited Phytoplankton Production and Its Bacterial Remineralization for Carbon and Oxygen Fluxes in the Baltic Sea

The Baltic Sea is prone to oxygen deficiency due to the restricted water exchange with the North Sea in coincidence with a high biological oxygen demand. The partitioning of organic carbon between respiration, accumulation and export is co-determined by phytoplankton primary production and its subsequent bacterial remineralization. Here, we investigated net phytoplankton primary production, heterotrophic bacterial biomass production and dark CO2 fixation by on-board incubations with radiolabeled tracers in the Baltic Proper and in the Gulf of Riga after the main spring bloom. Results show that low phytoplankton standing stocks of ≤1.6 µg chlorphyll a L-1 sustained net primary production of 161-724 mg C m-2 d-1 under nitrogen limitation. Estimates of bacterial carbon remineralization suggest that freshly produced organic carbon was supplied to the aphotic zone at all stations. In the southern Baltic Proper, net primary production exceeded the bacterial carbon demand in the upper mixed layer, suggesting that organic matter derived from nutrient-limited primary production was available for export to bacterial communities below the oxycline. On average, 46% of heterotrophic bacterial production was mediated in oxygen minimum zones, revealing the high importance of organic matter recycling under hypoxic and anoxic conditions for the carbon budget. Dark CO2 fixation of up to 4.33 µg C L-1 d-1 in sulfide-free waters equaled 9-54% of the co-inciding heterotrophic bacterial carbon demand and may have provided another organic carbon source for heterotrophic activity. Substantially higher dark CO2 fixation up to 25.46 µg C L-1 d-1 was determined in sulfidic waters. Since our study was conducted five months after the major Baltic inflow event in winter 2014/2015, potential effects of deep water ventilation could be investigated. In the Gotland Basin, heterotrophic bacterial production in renewed oxygen-rich bottom water was similar to that in the uplifted oxygen-deficient former bottom water, while it was significantly reduced in sulfidic waters. Hence, our results suggest that the removal of hydrogen sufide by inflow events has a high potential to increase bacterial carbon remineralization.

Operating at the very low end of the crassulacean acid metabolism spectrum: Sesuvium portulacastrum (Aizoaceae).

Demonstration of crassulacean acid metabolism (CAM) in species with low usage of this system relative to C3-photosynthetic CO2 assimilation can be challenging experimentally but provides crucial information on the early steps of CAM evolution. Here, weakly expressed CAM was detected in the well-known pantropical coastal, leaf-succulent herb Sesuvium portulacastrum, demonstrating that CAM is present in the Sesuvioideae, the only sub-family of the Aizoaceae in which it had not yet been shown conclusively. In outdoor plots in Panama, leaves and stems of S. portulacastrum consistently exhibited a small degree of nocturnal acidification which, in leaves, increased during the dry season. In potted plants, nocturnal acidification was mainly facultative, as levels of acidification increased in a reversible manner following the imposition of short-term water-stress. In drought-stressed plants, nocturnal net CO2 exchange approached the CO2-compensation point, consistent with low rates of CO2 dark fixation sufficient to eliminate respiratory carbon loss. Detection of low-level CAM in S. portulacastrum adds to the growing number of species that cannot be considered C3 plants sensu stricto, although they obtain CO2 principally via the C3 pathway. Knowledge about the presence/absence of low-level CAM is critical when assessing trajectories of CAM evolution in lineages. The genus Sesuvium is of particular interest because it also contains C4 species.

Sulfurimonas subgroup GD17 cells accumulate polyphosphate under fluctuating redox conditions in the Baltic Sea: possible implications for their ecology.

The central Baltic Sea is characterized by a pelagic redox zone exhibiting high dark CO2 fixation rates below the chemocline. These rates are mainly driven by chemolithoautotrophic and denitrifying Sulfurimonas GD17 subgroup cells which are motile and fast-reacting r-strategists. Baltic Sea redox zones are unstable and a measurable overlap of nitrate and reduced sulfur, essential for chemosynthesis, is often only available on small scales and short times due to local mixing events. This raises the question of how GD17 cells gain access to electron donors or acceptors over longer term periods and under substrate deficiency. One possible answer is that GD17 cells store high-energy-containing polyphosphate during favorable nutrient conditions to survive periods of nutrient starvation. We used scanning electron microscopy with energy-dispersive X-ray spectroscopy to investigate potential substrate enrichments in single GD17 cells collected from Baltic Sea redox zones. More specific substrate enrichment features were identified in experiments using Sulfurimonas gotlandica GD1T, a GD17 representative. Sulfurimonas cells accumulated polyphosphate both in situ and in vitro. Combined genome and culture-dependent analyses suggest that polyphosphate serves as an energy reservoir to maintain cellular integrity at unfavorable substrate conditions. This redox-independent energy supply would be a precondition for sustaining the r-strategy lifestyle of GD17 and may represent a newly identified survival strategy for chemolithoautotrophic prokaryotes occupying eutrophic redox zones.