14C Assimilation Research Articles

The path from root input to mineral-associated soil carbon is dictated by habitat-specific microbial traits and soil moisture

Soil microorganisms help transform plant inputs into mineral-associated soil organic carbon (SOC) – the largest and slowest-cycling pool of organic carbon on land. However, the microbial traits that influence this process are widely debated. While current theory and biogeochemical models have settled on carbon-use efficiency (CUE) and growth rate as positive predictors of mineral-associated SOC, empirical tests are sparse, with contradictory observations. Using 13C-labeling of an annual grass (Avena barbata) under two moisture regimes, we found that microbial traits associated with formation of 13C-mineral-associated SOC varied by soil habitat, as did active microbial taxa and SOC chemical composition. In the rhizosphere, bacterial-dominated communities with fast growth, high biomass, and high extracellular polymeric substance (EPS) production were positively associated with 13C-mineral-associated SOC. In contrast, the detritusphere held communities dominated by fungi and more filamentous bacteria, and with greater exoenzyme activity; there, 13C-mineral-associated SOC was associated with slower microbial growth and lower microbial biomass. CUE was a negative predictor of 13C-mineral-associated SOC in both habitats. Using 13C-quantitative stable isotope probing, we found that the majority of 13C assimilation in the rhizosphere and detritusphere at week 12 of the experiment was performed by very few bacterial and fungal taxa (3–5% of the total taxa that assimilated 13C). Several complementary chemical analyses (13C-NMR, FTICR-MS, and STXM-NEXAFS) suggested that SOC in the rhizosphere had a more oxidized chemical signature, while SOC in the detritusphere had a less oxidized, more lignin-like chemical signature. Our findings challenge current theory by demonstrating that microbial traits linked with mineral-associated SOC are not universal, but vary with soil habitat and moisture conditions, and are shaped by a small number of active taxa. Emerging SOC models that explicitly reflect these interactions may better predict SOC storage, since climate change causes shifts in soil moisture regimes and the ratio of living versus decaying roots.

Nitrogen fertilization enhances organic carbon accumulation in topsoil mainly by improving photosynthetic C assimilation in a salt marsh

Continuous nitrogen (N) loading alters plant growth and subsequently has the potential to impact soil organic carbon (SOC) accumulation in salt marshes. However, the knowledge gap of photosynthesized carbon (C) allocation in plant-soil-microbial systems hampers the quantification of C fluxes and the clarification of the mechanisms controlling the C budget under N loading in salt marsh ecosystems. To address this, we conducted an N fertilization field observation combined with a 5 h 13C-pulse labeling experiment in a salt marsh dominated by Suaeda. salsa (S. salsa) in the Yellow River Delta (YRD), China. N fertilization increased net 13C assimilation of S. Salsa by 277.97%, which was primarily allocated to aboveground biomass and SOC. However, N fertilization had little effect on 13C allocation to belowground biomass. Correlation analysis showed that 13C incorporation in soil was significantly and linearly correlated with 13C incorporation in shoots rather than in roots both in a 0 N (0 g N m−2 yr−1) and +N (20 g N m−2 yr−1) group. The results suggested that SOC increase under N fertilization was mainly due to an increased C assimilation rate and more efficient downward transfer of photosynthesized C. In addition, N fertilization strongly improved the 13C amounts in the chloroform-labile SOC component by 295.26%. However, the absolute increment of newly fix 13C mainly existed in the form of residual SOC, which had more tendency for burial in the soil. Thus, N fertilization enhanced SOC accumulation although C loss increased via belowground respiration. These results have important implications for predicting the carbon budget under further human-induced N loading.

Phosphorus Fertilization Boosts Mineral-Associated Soil Organic Carbon Formation Associated with Phagotrophic Protists.

Long-term fertilization affects soil organic C accumulation. A growing body of research has revealed critical roles of bacteria in soil organic C accumulation, particularly through mineral-associated organic C (MAOC) formation. Protists are essential components of soil microbiome, but the relationships between MAOC formation and protists under long-term fertilization remain unclear. Here, we used cropland soil from a long-term fertilization field trial and conducted two microcosm experiments with 13C-glucose addition to investigate the effects of N and P fertilizations on MAOC formation and the relationships with protists. The results showed that long-term fertilization (especially P fertilization) significantly (P < 0.05) increased 13C-MAOC content. Compared with P-deficient treatment, P replenishment enriched the number of protists (mainly Amoebozoa and Cercozoa) and bacteria (mainly Acidobacteriota, Bacteroidota, and Gammaproteobacteria), and significantly (P < 0.001) promoted the abundances of bacterial functional genes controlling C, N, P, and S metabolisms. The community composition of phagotrophic protists prominently (P < 0.001) correlated with the bacterial community composition, bacterial functional gene abundance, and 13C-MAOC content. Co-occurrence networks of phagotrophic protists and bacteria were more connected in soil with the N inoculum added than in soil with the NP inoculum added. P replenishment strengthened bacterial 13C assimilation (i.e., 13C-phospholipid fatty acid content), which negatively (P < 0.05) correlated with the number and relative abundance of phagotrophic Cercozoa. Together, these results suggested that P fertilization boosts MAOC formation associated with phagotrophic protists. Our study paves the way for future research to harness the potential of protists to promote belowground C accrual in agroecosystems.

Crop Productivity, Economic Advantage, and Photosynthetic Characteristics in a Corn-Peanut Intercropping System

Corn-peanut intercropping is an important element of China’s agricultural planting model as it confers ecological benefits and increases yield. The aim of this study was to explore the productivity differences between intercropping and monoculture by using the 13C isotope tracer labelling method. Corn hybrid Denghai 618 (DH618) and peanut variety Huayu 22 (HY22) were used as test materials under three planting methods, single corn, SM; single peanut, SP; and corn-peanut intercropping, IM and IP, respectively, during two growing seasons. The results showed that IM increased yield by 59.7% and 62.3% compared with SM, respectively. IP reduced yield by 31.3% and 32.3% compared with SP, respectively. IM significantly increased the photosynthetic rate, leaf area, 13C assimilation distribution, and dry matter accumulation of summer corn, which led to an increase in the kernel number and grain yield. The decrease in intercropped peanut yield was mainly caused by a decrease in the full-pod rate and number of pods per plant. The decrease in peanut yield did not affect the production of intercropping benefit due to the larger intercropping advantage and land equivalence ratio. Corn-peanut intercropping yielded greater economic benefits than monoculture. These results showed the utility of the peanut-corn intercropping model.

Acid rain reduces plant-photosynthesized carbon sequestration and soil microbial network complexity

Acid rain threatens the structure and function of terrestrial ecosystems; however, the mechanisms by which acid rain affects the photosynthesized carbon (C) fluxes and soil microbial communities are far less understood, thus impeding accurate projections of regional C flux in the plant-soil-atmosphere system. In this study, we performed an isotopic 13C labeling experiment to trace C footprints in a maize-soil system under acid rain pollution (pH 4.5 and 3.0; SO42−/NO3−= 2:1). Our results showed that acid rain exerted a negligible effect on total plant biomass as well as shoot biomass. Acid rain of pH 3.0 inhibited plant 13C assimilation and the flow of fixed 13C to the soil. Acid rain decreased soil total C and organic nitrogen (N) but increased inorganic N (i.e., nitrate-N) content. The acid rain of pH 3.0 enhanced soil bulk density, led to soil acidification, and promoted soil microbial diversity. However, acid rain reduced the connectivity and complexity of soil microbial network. Soil 13C content was mainly regulated by soil pH, ammonium-N, and root biomass. Our findings demonstrated that acid rain reduces photosynthesized C sequestration of maize-soil system and soil microbial taxa interactions.

Nitrogen limitation prevents the effects of iron or dust additions on biological carbon fixation in the Gulf of California

This paper reports the effect of dissolved iron (dFe) and dust additions on the Biological Carbon Fixation (BCF) rates in the surface layer of the central Gulf of California (GC). Two on deck experiments were conducted in the summer of 2016 at an oceanographic station located in the Guaymas Basin. Each experiment consisted in the incubation of natural phytoplankton assemblages collected at three distinct depths within the upper 50 m layer and amended either with iron (FeCl3) or dust leachate, followed by the quantification of BCF rates using the 13C assimilation method. A very warm (∼30 °C) water column strongly stratified and with reduced phytoplankton biomass (<1 mg chlorophyll a m−3) was indicative of an oligotrophic environment. In addition, the surface levels of NO3−+NO2− (<0.1 μM), dFe (1.71 ± 1.04 nM), as well as the Fe:N (78 ± 47 nmol μmol−1) and N:P (0.04 ± 0.01) ratios revealed that phytoplankton was under conditions of inorganic nitrogen limitation. BCF rates measured during the experiments ranged between 0.46 ± 0.04 and 6.24 ± 0.34 mg C m−3 h−1 with the highest values at the maximum of fluorescence and their vertical distribution was associated with the carbon biomass of picophytoplankton and diatoms. Despite the oligotrophic condition that predominated during the cruise, most of the Fe or dust additions did not show a significant effect (p > 0.05) on the magnitude of BCF rates, which was attributed to the fact that N, rather than Fe, was the limiting nutrient for phytoplankton production. However, Fe limitation cannot be completely ruled out as two samples (one for each treatment) showed a significant increase (p < 0.05) in BCF rates. We suggest that atmospheric supply of dust during the summer could play a relevant biological role maintaining high concentrations of dFe (and other bioactive metals) in the surface waters of central GC.

Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility

The skeleton of reef-building coral harbors diverse microbial communities that could compensate for metabolic deficiencies caused by the loss of algal endosymbionts, i.e., coral bleaching. However, it is unknown to what extent endolith taxonomic diversity and functional potential might contribute to thermal resilience. Here we exposed Goniastrea edwardsi and Porites lutea, two common reef‐building corals from the central Red Sea to a 17-day long heat stress. Using hyperspectral imaging, marker gene/metagenomic sequencing, and NanoSIMS, we characterized their endolithic microbiomes together with 15N and 13C assimilation of two skeletal compartments: the endolithic band directly below the coral tissue and the deep skeleton. The bleaching-resistant G. edwardsi was associated with endolithic microbiomes of greater functional diversity and redundancy that exhibited lower N and C assimilation than endoliths in the bleaching-sensitive P. lutea. We propose that the lower endolithic primary productivity in G. edwardsi can be attributed to the dominance of chemolithotrophs. Lower primary production within the skeleton may prevent unbalanced nutrient fluxes to coral tissues under heat stress, thereby preserving nutrient-limiting conditions characteristic of a stable coral-algal symbiosis. Our findings link coral endolithic microbiome structure and function to bleaching susceptibility, providing new avenues for understanding and eventually mitigating reef loss.

Investigating bacterial coupled assimilation of fertilizer‑nitrogen and crop residue‑carbon in upland soils by DNA-qSIP

Microbial immobilization of fertilizer nitrogen (N) can effectively reduce N losses in soil. However, the effects of crop residue on microbial assimilation of fertilizer-N and the underlying microbial mechanisms in upland soils are unclear. We evaluated the influence of maize residue (13C) addition on the microbial assimilation of ammonium-N (15N) in DNA from fertilizer, and quantified the bacterial 13C or 15N assimilation by quantitative stable isotope probing (DNA-qSIP). We found that the straw addition did increase total microbial assimilation of ammonium from fertilizer during the 2-week incubation. However, bacterial taxa varied in their responses to straw addition: Bacteriodetes and Proteobacteria accounted for large fractions of ammonium assimilation and their N assimilations were increased, while N assimilations of Acidobacteria were decreased. We revealed that highly 13C-labeled taxa were the main contributors of N assimilation under straw addition. The straw primarily enhanced the contributions of bacterial taxa to ammonium assimilation through increasing the extent of N assimilation, or enhancing the abundance of the N-assimilating bacterial taxa. Overall, our study elucidated an interaction between microbial assimilation of fertilizer-N and straw-C, showing a close element coupling of the keystone functional microbial taxa in N immobilization driven by organic carbon.

13C assimilation as well as functional gene abundance and expression elucidate the biodegradation of glyphosate in a field experiment

Glyphosate (N-phosphonomethylglycine; GLP) and its main metabolite AMPA (aminomethylphosphonic acid), are frequently detected in relatively high concentrations in European agricultural topsoils. Glyphosate has a high sorption affinity, yet it can be detected occasionally in groundwater. We hypothesized that shrinkage cracks occurring after dry periods could facilitate GLP transport to greater depths where subsoil conditions slow further microbial degradation. To test this hypothesis, we simulated a heavy rainfall event (HRE) on a clay-rich arable soil. We applied 2.1 kg ha−1 of 100% 13C3, 15N-labeled GLP one day before the simulated rainfall event. Microbial degradation of translocated GLP over a 21-day period was assessed by quantifying 13C incorporation into phospholipid fatty acids. Microbial degradation potential and activity were determined by quantifying the abundance and expression of functional genes involved in the two known degradation pathways of GLP; to AMPA (goxA) or sarcosine (sarc). We confirmed that goxA transcripts were elevated in the range of 4.23 x 105 copy numbers g−1 soil only one day after application. The increase in AMPA associated with a rise in goxA transcripts and goxA-harboring microorganisms indicated that the degradation pathway to AMPA dominated. Based on 13C-enrichment 3 h after the HRE, fungi appeared to initiate glyphosate degradation. At later time points, Gram+-bacteria proved to be the main degraders due to their higher 13C-incorporation. Once GLP reached the subsoil, degradation continued but more slowly. By comparing GLP distribution and its microbial degradation in macropores and in the bulk soil, we demonstrated different time- and depth-dependent GLP degradation dynamics in macropores. This indicates the need for field studies in which soil properties relevant to GLP degradation are related to limiting environmental conditions, providing a realistic assessment of GLP fate in soils.

Plants with arbuscular mycorrhizal fungi efficiently acquire Nitrogen from substrate additions by shaping the decomposer community composition and their net plant carbon demand

AimsWe investigated the role of plants and their plant-derived carbon in shaping the microbial community that decomposes substrates and traced the return of nutrients from decomposition back to plant shoots in order to understand the importance of plants for ecosystem element cycling.MethodsWe performed a greenhouse experiment having plant communities with and without arbuscular mycorrhizal fungi (AMF) and ingrowth cores that held different 15N labeled substrates. We determined the microbial community structure using molecular sequencing and the net assimilation of plant carbon into soil microorganisms using a 13CO2 pulse and 13C measurements of microbial biomarkers. We determined the return of nitrogen back to the shoots using the 15N signal, which was provided from the decomposition of the substrate added to the ingrowth cores.ResultsWe observed that the microbial community composition in the ingrowth cores and their net 13C assimilation depended on the presence of AMF and the added substrate. Both plant communities had similar 15N uptake into their shoots, but the net N uptake cost was significantly lower in presence of AMF. In the presence of AMF also lower net N uptake cost was observed for the decomposition of plant-derived and microorganism-derived substrates compared to inorganic nitrogen suggesting that AMF actively controls the decomposer comunity and their carbon demand.ConclusionOur results identify for the first time a functional overlap of soil microorganisms as identical substrate is decomposed by different microorganisms suggesting functional redundancy of microbial communities. In consequence a better understanding of ecosystem element cycling can only be achieved when the whole plant-microorganism-organic matter-soil continuum is investigated.

Straw Incorporation Effects on Net Photosynthetic Carbon Assimilation and Maize Growth

Returning straw into soil could increase soil organic carbon (SOC) and promote crop growth. However, little has been reported on the source of C for increased SOC (straw C or crop photosynthetic C). To investigate the assimilation of photosynthetic C and its distribution in soil in the maize growth season, we set up a 1-year 13C pulse-labeling experiment in a consecutive maize-straw-returning long-term trial. Four treatments were included: no straw return (control), straw mulching on the soil surface (cover), return in 0–20 cm layer (shallow), and 20–40 cm layer (deep). We found that the deep straw incorporation significantly (P &amp;lt; 0.05) increased maize 100-grain weight (by 7.8%), yield in the coming year (by 10.5%), and SOC (by 13.4%) compared with the control. During the growing season, the deep straw incorporation increased photosynthetic 13C assimilation in shoots by 17.4% and the partitioning of photosynthetic 13C to soil by 7.9% at early jointing, and by 11.5% at maturity. The contribution of photosynthetic C to microbial biomass C (MBC) and dissolved organic C (DOC) was highest at jointing, and at harvest amounted to 39.1 % of MBC and 28.8% of DOC. The results highlighted the importance of regulating the soil carbon dynamics via the deep straw return strategy. In conclusion, deep straw incorporation significantly increased photosynthetic efficiency and facilitated partitioning of photosynthetic C to roots and soil, thus promoting maize growth and yield.

13c Assimilation as Well as Functional Gene Abundance and Expression Elucidate the Biodegradation of Glyphosate in a Field Experiment

13c Assimilation as Well as Functional Gene Abundance and Expression Elucidate the Biodegradation of Glyphosate in a Field Experiment

Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling

Soil microorganisms determine the fate of soil organic matter (SOM), and their activities compose a major component of the global carbon (C) cycle. We employed a multisubstrate, DNA-stable isotope probing experiment to track bacterial assimilation of C derived from distinct sources that varied in bioavailability. This approach allowed us to measure microbial contributions to SOM processing by measuring the C assimilation dynamics of diverse microorganisms as they interacted within soil. We identified and tracked 1,286 bacterial taxa that assimilated 13C in an agricultural soil over a period of 48 d. Overall 13C-assimilation dynamics of bacterial taxa, defined by the source and timing of the 13C they assimilated, exhibited low phylogenetic conservation. We identified bacterial guilds composed of taxa that had similar 13C assimilation dynamics. We show that C-source bioavailability explained significant variation in both C mineralization dynamics and guild structure, and that the growth dynamics of bacterial guilds differed significantly in response to C addition. We also demonstrate that the guild structure explains significant variation in the biogeographical distribution of bacteria at continental and global scales. These results suggest that an understanding of in situ growth dynamics is essential for understanding microbial contributions to soil C cycling. We interpret these findings in the context of bacterial life history strategies and their relationship to terrestrial C cycling.

Identification of the phylotypes involved in cis-dichloroethene and 1,4-dioxane biodegradation in soil microcosms

Co-contamination with chlorinated compounds and 1,4-dioxane has been reported at many sites. Recently, there has been an increased interest in bioremediation because of the potential to degrade multiple contaminants concurrently. Towards improving bioremediation efficacy, the current study examined laboratory microcosms (inoculated separately with two soils) to determine the phylotypes and functional genes associated with the biodegradation of two common co-contaminants (cis-dichloroethene [cDCE] and 1,4-dioxane). The impact of amending microcosms with lactate on cDCE and 1,4-dioxane biodegradation was also investigated. The presence of either lactate or cDCE did not impact 1,4-dioxane biodegradation one of the two soils. Lactate appeared to improve the initiation of the biological removal of cDCE in microcosms inoculated with either soil. Stable isotope probing (SIP) was then used to determine which phylotypes were actively involved in carbon uptake from cDCE and 1,4-dioxane in both soil communities. The most enriched phylotypes for 13C assimilation from 1,4-dioxane included Rhodopseudomonas and Rhodanobacter. Propane monooxygenase was predicted (by PICRUSt2) to be dominant in the 1,4-dioxane amended microbial communities and propane monooxygenase gene abundance values correlated with other enriched (but less abundant) phylotypes for 13C-1,4-dioxane assimilation. The dominant enriched phylotypes for 13C assimilation from cDCE included Bacteriovorax, Pseudomonas and Sphingomonas. In the cDCE amended soil microcosms, PICRUSt2 predicted the presence of DNA encoding glutathione S-transferase (a known cDCE upregulated enzyme). Overall, the work demonstrated concurrent removal of cDCE and 1,4-dioxane by indigenous soil microbial communities and the enhancement of cDCE removal by lactate. The data generated on the phylotypes responsible for carbon uptake (as determined by SIP) could be incorporated into diagnostic molecular methods for site characterization. The results suggest concurrent biodegradation of cDCE and 1,4-dioxane should be considered for chlorinated solvent site remediation.

Bacterial contribution to 17β-estradiol mineralization in lake sediment as revealed by 13C-DNA stable isotope probing

The accumulation of estrogens in aquatic environments has drawn increasing public concern due to their adverse effects on aquatic ecosystems and human health. Bacteria play important roles in eliminating estrogens from the environment, but knowledge of the identity and functions of the microorganisms involved in metabolizing these steroid hormones in the natural microbial communities is lacking. Here, we added 13C-17β-estradiol (13C-E2) to sediments collected from Zhushan (ZS) Bay, Meiliang (ML) Bay, Gonghu (GH) Bay, and the central area (CA) of the Taihu Lake. The indigenous assimilators of E2 in the sediments were recognized using 13C-DNA stable isotope probing (DNA-SIP), and their effects on 13C-E2 mineralization were studied under aerobic condition. During the 30-day incubation period, ZS Bay had the highest cumulative percentage of 13C-E2 mineralization to 13CO2 (65.5%), while CA presented the lowest (51.4%). Based on DNA-SIP, we saw that Novosphingobium, Ralstonia, Pseudomonas, Sphingomonas, Nitrosomonas, and Alcaligenes were involved in E2-derived 13C assimilation for the entire incubation period. Acinetobacter, Flavobacterium, and Mycobacterium only assimilated 13C for the first half of the incubation. H16 was identified as an E2 assimilator for the first time in this study. In addition, the temporal changes in assimilator abundances during the incubation period indicated that these genera played dominant roles at different stages in the process of E2 biodegradation. The bacteria engaged in the assimilation of E2 in situ were identified, and the rate of increase in the relative abundance of assimilators was significantly (P < 0.05) and positively correlated with the E2 mineralization in sediments. This information enhances our knowledge of in situ E2 biodegradation and provides a potential resource that could be used to eliminate estrogens in sediments.

Effects of zinc levels on synthesis and translocation of 13C-photoassimilates in leaves to fruit of apple during fruit expanding stage

To explore the effects of zinc levels on the synthesis and translocation of photosynthetic products from leaves to fruits, and to lay a theoretical foundation for improving fruit quality through zinc supplementation during the critical period of apple fruit development, a field experiment was carried out with a eight-year old 'Hanfu'/GM256/Malus baccata Borkh apple. We used the 13C tracer method to examine the effects of different zinc levels (ZnSO4·H2O 0, 0.1%, 0.2%, 0.3%, 0.4%, expressed by CK, Zn1, Zn2, Zn3, Zn4, respectively) on translocation of photosynthate to fruit during the stage of fruit expanding. The results showed that, with increasing zinc concentration, Rubisco enzyme activity, net photosynthetic rate, sorbitol and sucrose content, sorbitol 6-phosphate dehydrogenase, and sucrose phosphate synthase enzyme activities of leaves first increased and then decreased, with the highest values being observed in Zn3 treatment. Zn3 treatment significantly increased the 13C assimilation capability of leaves. Compared with other treatments, the 13C of self-retention (labeled leaves and labeled branches) was lowest in Zn3 treatment (61.2%) and the output of 13C photoassimilates was highest in Zn3 treatment (38.8%). 13C absorption of apple fruit showed a trend of Zn3 ＞ Zn2 ＞ Zn4 ＞ Zn1 ＞ CK. In summary, foliar zinc application under appropriate concentration (0.3% ZnSO4·H2O) enhanced photosynthesis, increased the assimilation capability of leaves, and promoted the directional transportation of photosynthate to fruit.

Linking microbial taxa and the effect of mineral nitrogen forms on residue decomposition at the early stage in arable soil by DNA-qSIP

The decomposition of crop residues represents the largest organic carbon (C) input into agricultural ecosystems, and plays an important role in soil C sequestration and soil fertility. However, how different forms of mineral nitrogen (N) influence the decomposition of these residues, or their associated active microbes, is poorly understood. In this study, we investigated the impacts of ammonium ((NH4)2SO4) and nitrate (KNO3) on the early stages (14 days) of decomposition of highly enriched 13C-labeled (13C atom% = 77.0%) maize residues. Further, we characterized the contributions of various bacterial and archaeal taxa using quantitative stable isotope probing (qSIP). To our surprise, we found that the majority of measured parameters including 13C soil respiration, total 13C microbial assimilation in soil DNA, as well as the diversity and structure of these microbial communities, were not significantly different between these two N forms during our 2-week incubation. Slight differences were observed however, in the activity of straw-metabolizing microbes. The qSIP revealed variability in 13C assimilation (excess atom fraction, EAF) among different microbial taxa at the operational taxonomic unit (OTU) level, with Proteobacteria, Bacteroidetes, and Verrucomicrobia being the most intensively 13C-labeled phyla, suggesting their potentially dominant roles in residue decomposition. However, only the 13C EAF of Thaumarchaeota (genus Nitrososphaera) was significantly higher in the ammonium treatment than in the nitrate treatment. The Nitrososphaera might indirectly participate in the decomposition of residues by fixing CO2 or by directly incorporate 13C from organic matter. These results reveal a quantitative overview of the contribution of bacteria and archaea to residue decomposition. Further, we document that the similar effect of nitrate and ammonium on residue decomposition at the early stages is likely due to the unchanged activity of predominant bacterial taxa with the two N forms.

A database of ocean primary productivity from the 14C method

AbstractThe database on ocean primary productivity comprises over two decades (1985–2008) of data that the authors have participated in collecting, using the assimilation of inorganic 14C through photosynthesis, in incubations carried out in situ. The dataset is perhaps unique in that it uses, overwhelmingly, consistent methodology while covering a wide geographic range. Ancillary data are included. Using the database, it is hoped that investigators can test for the relationships among the environmental drivers for ocean productivity, the meaning of the 14C method in terms of phytoplankton physiology and the dynamics in the water column, and as a resource for further development of productivity algorithms using satellite ocean color imagery.

Differential processing of dissolved and particulate organic matter by deep-sea sponges and their microbial symbionts

Deep-sea sponges create hotspots of biodiversity and biological activity in the otherwise barren deep-sea. However, it remains elusive how sponge hosts and their microbial symbionts acquire and process food in these food-limited environments. Therefore, we traced the processing (i.e. assimilation and respiration) of 13C- and 15N-enriched dissolved organic matter (DOM) and bacteria by three dominant North Atlantic deep-sea sponges: the high microbial abundance (HMA) demosponge Geodia barretti, the low microbial abundance (LMA) demosponge Hymedesmia paupertas, and the LMA hexactinellid Vazella pourtalesii. We also assessed the assimilation of both food sources into sponge- and bacteria-specific phospholipid-derived fatty acid (PLFA) biomarkers. All sponges were capable of assimilating DOM as well as bacteria. However, processing of the two food sources differed considerably between the tested species: the DOM assimilation-to-respiration efficiency was highest for the HMA sponge, yet uptake rates were 4–5 times lower compared to LMA sponges. In contrast, bacteria were assimilated most efficiently and at the highest rate by the hexactinellid compared to the demosponges. Our results indicate that phylogeny and functional traits (e.g., abundance of microbial symbionts, morphology) influence food preferences and diet composition of sponges, which further helps to understand their role as key ecosystem engineers of deep-sea habitats.

Biodegradation of Pesticides at the Limit: Kinetics and Microbial Substrate Use at Low Concentrations.

The objective of our study was to test whether limited microbial degradation at low pesticide concentrations could explain the discrepancy between overall degradability demonstrated in laboratory tests and their actual persistence in the environment. Studies on pesticide degradation are often performed using unrealistically high application rates seldom found in natural environments. Nevertheless, biodegradation rates determined for higher pesticide doses cannot necessarily be extrapolated to lower concentrations. In this context, we wanted to (i) compare the kinetics of pesticide degradation at different concentrations in arable land and (ii) clarify whether there is a concentration threshold below which the expression of the functional genes involved in the degradation pathway is inhibited without further pesticide degradation taking place. We set up an incubation experiment for four weeks using 14C-ring labeled 2-methyl-4-chlorophenoxyacetic acid (MCPA) as a model compound in concentrations from 30 to 20,000 μg kg–1 soil. To quantify the abundance of putative microorganisms involved in MCPA degradation and their degradation activity, tfdA gene copy numbers (DNA) and transcripts (mRNA) were determined by quantitative real-time PCR. Mineralization dynamics of MCPA derived-C were analyzed by monitoring 14CO2 production and 14C assimilation by soil microorganisms. We identified two different concentration thresholds for growth and activity with respect to MCPA degradation using tfdA gene and mRNA transcript abundance as growth and activity indices, respectively. The tfdA gene expression started to increase between 1,000 and 5,000 μg MCPA kg–1 dry soil, but an actual increase in tfdA sequences could only be determined at a concentration of 20,000 μg. Accordingly, we observed a clear shift from catabolic to anabolic utilization of MCPA-derived C in the concentration range of 1,000 to 5,000 μg kg–1. Concentrations ≥1,000 μg kg–1 were mainly associated with delayed mineralization, while concentrations ≤1,000 μg kg–1 showed rapid absolute dissipation. The persistence of pesticides at low concentrations cannot, therefore, be explained by the absence of functional gene expression. Nevertheless, significant differences in the degradation kinetics of MCPA between low and high pesticide concentrations illustrate the need for studies investigating pesticide degradation at environmentally relevant concentrations.