Organic Carbon Metabolism Research Articles

Aqueous system-level processes and prokaryote assemblages in the ferruginous and sulfate-rich bottom waters of a post-mining lake

Abstract. In the low-nutrient, redox-stratified Lake Medard (Czechia), reductive Fe(III) dissolution outpaces sulfide generation from microbial sulfate reduction (MSR) and ferruginous conditions occur without quantitative sulfate depletion. The lake currently has marked overlapping C, N, S, Mn and Fe cycles occurring in the anoxic portion of the water column. This feature is unusual in stable, natural, redox-stratified lacustrine systems where at least one of these biogeochemical cycles is functionally diminished or undergoes minimal transformations because of the dominance of another component or other components. Therefore, this post-mining lake has scientific value for (i) testing emerging hypotheses on how such interlinked biogeochemical cycles operate during transitional redox states and (ii) acquiring insight into redox proxy signals of ferruginous sediments underlying a sulfatic and ferruginous water column. An isotopically constrained estimate of the rates of sulfate reduction (SRRs) suggests that despite high genetic potential, this respiration pathway may be limited by the rather low amounts of metabolizable organic carbon. This points to substrate competition exerted by iron- and nitrogen-respiring prokaryotes. Yet, the planktonic microbial succession across the nitrogenous and ferruginous zones also indicates genetic potential for chemolithotrophic sulfur oxidation. Therefore, our SRR estimates could rather be portraying high rates of anoxic sulfide oxidation to sulfate, probably accompanied by microbially induced disproportionation of S intermediates. Near and at the anoxic sediment–water interface, vigorous sulfur cycling can be fuelled by ferric and manganic particulate matter and redeposited siderite stocks. Sulfur oxidation and disproportionation then appear to prevent substantial stabilization of iron monosulfides as pyrite but enable the interstitial precipitation of microcrystalline equant gypsum. This latter mineral isotopically recorded sulfur oxidation proceeding at near equilibrium with the ambient anoxic waters, whilst authigenic pyrite sulfur displays a 38 ‰ to 27 ‰ isotopic offset from ambient sulfate, suggestive of incomplete MSR and open sulfur cycling. Pyrite-sulfur fractionation decreases with increased reducible reactive iron in the sediment. In the absence of ferruginous coastal zones today affected by post-depositional sulfate fluxes, the current water column redox stratification in the post-mining Lake Medard is thought relevant for refining interpretations pertaining to the onset of widespread redox-stratified states across ancient nearshore depositional systems.

Positive contribution of macrofaunal biodiversity to secondary production and seagrass carbon metabolism.

Coastal vegetated habitats such as seagrasses are known to play a critical role in carbon cycling and the potential to mitigate climate change, as blue carbon habitats have been repeatedly highlighted. However, little information is known about the role of associated macrofauna communities on the dynamics of critical processes of seagrass carbon metabolism (e.g., respiration, turnover, and production). We conducted a field study across a spatial gradient of seagrass meadows involving variable environmental conditions and macrobenthic diversity to investigate (1) the relationship between macrofauna biodiversity and secondary production (i.e., consumer incorporation of organic matter per time unit), and (2) the role of macrofauna communities in seagrass organic carbon metabolism (i.e., respiration and primary production). We show that, although several environmental factors influence secondary production, macrofauna biodiversity controls the range of local seagrass secondary production. We demonstrate that macrofauna respiration rates were responsible for almost 40% of the overall seafloor community respiration. Macrofauna represented on average >25% of the total benthic organic C stocks, high secondary production that is likely to become available to upper trophic levels of the coastal food web. Our findings support the role of macrofauna biodiversity in maintaining productive ecosystems, implying that biodiversity loss due to ongoing environmental change yields less productive seagrass ecosystems. Therefore, the assessment of carbon dynamics in coastal habitats should include associated macrofauna biodiversity elements if we aim to obtain robust estimates of global carbon budgets required to implement management actions for the sustainable functioning of the world's coasts.

Rice straw carbon mineralization is affected by the timing of exogenous glucose addition in flooded paddy soil

Crop straw amendment is a farm management approach for enhancing soil carbon sequestration. Moreover, crop straw residue decomposition rates are affected by irregular exogenous organic carbon secretion or metabolism such as that from root exudates or microbial metabolites. To quantify the mineralization rate of straw residue affected by exogenous organic carbon addition and elucidate the underlying mechanisms, in this study, a total of 0.5 g 13C- labeled dry rice straw was added into pre-incubated soil (equivalent to 200 g dry soil) and incubated for 20 days. Then,1mL of a solution with 50 mg glucose was added only once into the soil on day 21 (G(1a)) or day 35 (G(1b)), twice with 25 mg glucose every 14 days (G(2)) or four times with 12.5 mg glucose every 7 days (G(4)). Soil without glucose addition served as a control. The frequent addition of glucose induced higher soil respiration than that induced by only one addition, and stimulated the mineralization of rice straw carbon compared to that in the control in the following order: G(4) (14.6%) > G(1a) (12.7%) > G(2) (12.3%) > G(1b) (11.2%) = control (11.2%). In general, frequent addition of glucose decreased the soil redox potential (Eh) and fungi to bacteria ratio. Structural equation modeling analysis showed that the rice straw carbon mineralization rate was positively correlated with the 13C-dissolved organic carbon (13C-DOC) content and negatively regulated by Eh. Microbial bioactivity exerted indirect positive effects on rice straw carbon mineralization by influencing the 13C-DOC content. A decrease in the fungi to bacteria ratio induced by frequent addition of glucose improved the microbial bioactivity and enhanced rice straw carbon mineralization. Our results suggested that single exogenous organic carbon additions may underestimate residue or soil organic matter decomposition rates in the field.

Simulating Microbial Functional Diversity Dynamics in Agricultural Soils: An Individual Based Modeling Approach

New agricultural soil model approaches based on the microbiome dynamics must be considered as they can contribute to understand microbiological soil processes directly linked to substrate metabolism and the influence of these processes on plant growth. The present work presents an approach to the modelling of the interactions of the soil microbial functional diversity with the plant in terms of functions associated to specific processes of organic Carbon and Nitrogen metabolism. The substrates transformations arising in the organic matter that enters as a part of an agricultural scheme are the base for define this metabolism. As result, it has been possible to simulate a rhizospheric soil based on the concept of complex system dynamics and Individual Based Modeling known too as Agent-Based Modeling in an agricultural management context. The explicit definition of the microbiome functional diversity and the processing of the structural elements Carbon and Nitrogen, allowed representing the functional dynamics of this complex system composed by microorganisms, Carbon, Nitrogen and the plant. The variables that reflect the biology and the adaptation to the rhizospheric environment characterized the microorganisms and the assemblage community patterns in time. The main simulations output are system glucose and nitrate levels and an approach to plant growth, all resultant from the metabolic process of the considered Carbon and Nitrogen consortia. The results indicate that the microorganism’s diversity assemblages and its functional expression have a fundamental role in terms of plant growth.

自然增温对南亚热带森林土壤微生物群落与有机碳代谢功能基因的影响

基于海拔高度下降气温上升的关系，将模拟的生态系统（含植物和土壤）从高海拔整体移位至低海拔地区，实现自然增温的效果。通过对自然增温条件下土壤环境因子及其相关理化性质的动态监测，结合磷脂脂肪酸分析与宏基因组学方法，测定土壤微生物群落结构以及与土壤有机碳分解相关基因丰度，探究自然增温对鼎湖山南亚热带山地常绿阔叶林土壤有机碳代谢的影响及其微生物学机制。结果表明：（1）增温处理显著改变了0-10 cm土壤温度与湿度：2016-2018年间土壤温度显著上升2.48℃，湿度显著下降23.93%。（2）增温处理下，干季土壤有机碳含量与湿季土壤硝态氮含量显著降低，其他土壤理化因子无显著变化。（3）增温处理下，干季和湿季土壤微生物群落结构发生改变，且湿季变化显著。土壤湿度是影响干季和湿季土壤微生物群落结构变化的主要因子，解释了干季50.2%的变异度与湿季79.2%的变异度。（4）宏基因组结果表示：增温抑制了干季山地常绿阔叶林土壤有机碳代谢基因丰度，增强了湿季山地常绿阔叶林土壤有机碳代谢基因丰度。以上结果表明，增温通过改变土壤微生物生物量和群落结构以及有机碳代谢相关功能基因的丰度，最终影响南亚热带山地常绿阔叶林土壤有机碳代谢过程。;Global warming is one of the environmental problems that cannot be ignored in the world today, which has significant impacts on soil carbon dynamics and soil microorganisms. Soil microorganisms affect the soil nutrient cycling process and play a leading role in the net carbon balance of terrestrial ecosystems. Further exploration of microbial responses to climate warming is important for predicting the feedback and carbon budget of terrestrial ecosystems in warmer climates. In this study, soil organic carbon content and microorganisms were investigated in a natural warming experiment using a whole ecosystem transplanting approach. Plots of plants and soil in a subtropical mountain evergreen broadleaf forest at high altitude (600 m asl) were moved to low altitude (30 m asl) in Dinghu Mountain to experience natural warming treatment. Plots with similar plants and soil at the high altitude were used as the control. To explore the effect of natural warming on soil organic carbon metabolism and its microbiological mechanism, soil physical and chemical properties, soil organic carbon, and soil microbial community structure were measured for the control and warmed plots. Meta-genomic method was used for soil microbial community structure and abundance of genes involved in soil organic carbon decomposition. Results showed that:(1) warming treatment significantly changed soil temperature and moisture of the 0-10 cm soil layer. From 2016 to 2018, the soil temperature was significantly increased by 2.48℃, and the soil moisture was significantly decreased by 23.93% (relative change). (2) Warming treatment significantly reduced soil organic carbon content in the dry season and the soil nitrate nitrogen content in the wet season, while other soil physical and chemical factors had no significant changes under warming treatment. (3) Warming treatment changed the soil microbial community structure in both dry and wet seasons, and the change was significant in wet season. The results of principal component analysis showed that soil moisture was the main factor affecting the variation of soil microbial community structure in dry season and wet season, which explained the variation degree of 50.2% in dry season and 79.2% in wet season. (4) The metagenomic analysis showed that increasing temperature inhibited the abundance of soil organic carbon metabolism genes of mountain evergreen broadleaf forest in the dry season, and enhanced them in the wet season. Our results showed that although warming treatment did not significantly change soil microbial biomass in the subtropical mountain evergreen broadleaf forest, it reduced soil organic carbon by changing soil microbial community structure and abundance, and significantly affected soil organic carbon metabolic processes and ecosystem carbon cycling.

Microbial processing of autochthonous organic matter controls the biodegradation of 17α-ethinylestradiol in lake sediments under anoxic conditions

The decay of algal biomass and aquatic plants in freshwater lakes leads to the overproduction of autochthonous organic matter (OM) and the exhaustion of dissolved oxygen, impacting the microbial community and subsequent biodegradation of emerging contaminants in sediment. This study explored how the microbial processing of aquatic plant- and algal-derived OM (POM and AOM) mediates 17α-ethinylestradiol (EE2) biodegradation in the anoxic sediments of Lake Taihu in China. In four months of microcosm incubations, the increased concentrations of protein-like substances in AOM and POM exhibited temporary activation on microbial metabolic enzyme activity (fluorescein diacetate hydrolase and dehydrogenase) and significantly promoted the carbon mineralization with iron reduction (P < 0.001). These in turn increased the EE2 biodegradation efficiency to 77–90 ng g−1 in the anoxic sediment. However, a higher EE2 biodegradation of 109 ng g−1 was achieved with the humic acid augmentation containing more quinone-like compounds, showing a weaker substrate-priming effect but accelerated redox cycling of iron and organic substrates in the later period of incubation. The microbial analysis further revealed that the quinone-like compounds in OM were more closely associated with microbial electron transfer and strengthened their interspecies syntrophic cooperation favorable to contaminant biodegradation, even though the connective members exposed to protein-like components upregulated more functional genes related to organic carbon and xenobiotics metabolism and biodegradation. Our findings will help predict the fate of estrogens in various sedimentary environments under increasing eutrophication and further climate change scenarios.

320 Liver Transcriptome Analysis Reveals Important Genes Involved in the Feed Efficiency of Lactating Cows Fed a High and Low Starch Diet

Abstract The objectives of this study were to identify different gene expression and metabolic pathways in the liver associated with feed efficiency of lactating cows fed high or low starch diets. Ten lactating cows were involved in a cross-over design experiment consisting of two 56-d treatment periods with 11-d diet adaptation fed either high starch (HS; 27% starch) or low starch (LS; 13% starch) diets. Feed efficiency, measured by residual feed intake (RFI), was estimated based on the difference between observed and expected metabolizable energy intake within each experimental period. The 3 highest RFI cows were considered high RFI (HRFI), the 3 lowest RFI cows were considered low (LRFI), and the remaining 4 cows were considered medium (MRFI) in each experimental period. Total RNA was used for next-generation RNA sequencing analysis. Raw reads were mapped to the cattle genome (UMD3.1) using STAR. Differential gene expression analysis was done using Cufflinks. We discovered 642 differentially expressed genes (DEGs) between HS and LS (FDR&amp;lt; 0.05) with 240 genes upregulated and 402 genes downregulated for HS versus LS diet. Via gene-set enrichment analysis (GSEA) analysis (FDR&amp;lt; 0.05), these genes were enriched in 25 gene ontology (GO) pathways related to mitochondria components and 4 GO biological processes involved in peptide metabolism. There were 1427 DEGs impacted by RFI (FDR&amp;lt; 0.05), of which 829 were upregulated, and 598 were downregulated in LRFI compared to HRFI. The 6 GO biological processes enriched by these genes were mainly related to organic substrate metabolism processing and carbon metabolism (FDR&amp;lt; 0.05). Between the DEGs affected by diet and RFI, 522 DGEs were unique to diet and 1307 DEGs were unique to RFI. Our results suggested that genes contributing to different RFIs and the ones associated with the dietary starch treatment may impact distinct pathways. Further functional annotation of these genes may improve feed efficiency.

Shift in archaeal community along a soil profile in coastal wheat‐maize rotation fields of different reclamation ages

AbstractCoastal mudflats reclamation activities show a strong influence on soil properties and microbial community activity, which drive soil carbon and nitrogen cycling. Studies have found there is a shift of bacterial community with reclamation time. However, effects of reclamation time on the soil archaeal community are still largely unknown. Here, we determined soil properties and archaeal community in the soil profiles (0–15, 15–30, 30–45 cm) of different reclaimed sites with different reclamation ages (R12: 12‐year; R38: 38‐year; R68: 68‐year; R100: 100‐year) in Rudong County, Jiangsu, China. Soil archaeal communities were identified via Illumina high‐throughput sequencing. Soil archaeal communities were dominated by two phyla, the Crenarchaeota (82.1–93.3%) and Thermoplasmatota (4.2–17.9%), which are associated with nitrogen cycle (Nitrosopumilaceae, Nitrososphaeraceae, and Nitrosotaleaceae) and organic carbon metabolism (Marine_Group_II), respectively. Ammonia oxidizing archaea showed a divergent response to the reclamation, i.e. Nitrosotaleaceae increased with reclamation time whereas Nitrosopumilaceae showed a decreasing trend. Soil total carbon, total nitrogen, pH, EC, C:N ratio, NO3−‐N content, soil moisture, depth, and reclamation age determined archaeal community distribution in our reclaimed sites. Our findings suggest that both reclamation time and soil depth significantly shaped the archaeal community composition, and then in turn modulated soil carbon and nitrogen cycling in the reclaimed mudflats.

Metagenomic analysis of facilitation mechanism for azo dye reactive red 2 degradation with the dosage of ferroferric oxide

Biological degradation of azo dyes and their intermediates requires a relatively long reaction duration due to their refractory characteristics. To enhance the azo dye degradation, the effects of ferroferric oxide (Fe3O4) on organic carbon metabolism, azo dye degradation, and microbial community structures were investigated through metagenomic analysis. Microorganisms possessing the azo dye-degradation ability changed from Bacillus, Aeromonas, and Lysobacter to Acinetobacter and Desulfovibrio when the Fe3O4 dosage increased from 0 g/L to 15 g/L. Geobacter and Staphylococcus were the most important bacteria involving in organic carbon metabolism, electron transfer, and azo dye degradation, and the dosage of Fe3O4 could enrich both microorganisms and enhance system performance. The facilitation mechanism with the dosage of Fe3O4 could be attributed to the increase of extracellular electron transfer rate and the enrichment of functional microorganisms.

Invertebrate and Microbial Response to Hyporheic Restoration of an Urban Stream

All cities face complex challenges managing urban stormwater while also protecting urban water bodies. Green stormwater infrastructure and process-based restoration offer alternative strategies that prioritize watershed connectivity. We report on a new urban floodplain restoration technique being tested in the City of Seattle, USA: an engineered hyporheic zone. The hyporheic zone has long been an overlooked component in floodplain restoration. Yet this subsurface area offers enormous potential for stormwater amelioration and is a critical component of healthy streams. From 2014 to 2017, we measured hyporheic temperature, nutrients, and microbial and invertebrate communities at three paired stream reaches with and without hyporheic restoration. At two of the three pairs, water temperature was significantly lower at the restored reach, while dissolved organic carbon and microbial metabolism were higher. Hyporheic invertebrate density and taxa richness were significantly higher across all three restored reaches. These are some of the first quantified responses of hyporheic biological communities to restoration. Our results complement earlier reports of enhanced hydrologic and chemical functioning of the engineered hyporheic zone. Together, this research demonstrates that incorporation of hyporheic design elements in floodplain restoration can enhance temperature moderation, habitat diversity, contaminant filtration, and the biological health of urban streams.

Investigation of carbon and energy metabolic mechanism of mixotrophy in Chromochloris zofingiensis

BackgroundMixotrophy can confer a higher growth rate than the sum of photoautotrophy and heterotrophy in many microalgal species. Thus, it has been applied to biodiesel production and wastewater utilization. However, its carbon and energy metabolic mechanism is currently poorly understood.ResultsTo elucidate underlying carbon and energy metabolic mechanism of mixotrophy, Chromochloris zofingiensis was employed in the present study. Photosynthesis and glucose metabolism were found to operate in a dynamic balance during mixotrophic cultivation, the enhancement of one led to the lowering of the other. Furthermore, compared with photoautotrophy, non-photochemical quenching and photorespiration, considered by many as energy dissipation processes, were significantly reduced under mixotrophy. Comparative transcriptome analysis suggested that the intermediates of glycolysis could directly enter the chloroplast and replace RuBisCO-fixed CO2 to provide carbon sources for chloroplast organic carbon metabolism under mixotrophy. Therefore, the photosynthesis rate-limiting enzyme, RuBisCO, was skipped, allowing for more efficient utilization of photoreaction-derived energy. Besides, compared with heterotrophy, photoreaction-derived ATP reduced the need for TCA-derived ATP, so the glucose decomposition was reduced, which led to higher biomass yield on glucose. Based on these results, a mixotrophic metabolic mechanism was identified.ConclusionsOur results demonstrate that the intermediates of glycolysis could directly enter the chloroplast and replace RuBisCO-fixed CO2 to provide carbon for photosynthesis in mixotrophy. Therefore, the photosynthesis rate-limiting enzyme, RuBisCO, was skipped in mixotrophy, which could reduce energy waste of photosynthesis while promote cell growth. This finding provides a foundation for future studies on mixotrophic biomass production and photosynthetic metabolism.

Enhancing nitrate removal from wastewater by integrating heterotrophic and autotrophic denitrification coupled manganese oxidation process (IHAD-MnO): Internal carbon utilization performance

Due to cause the deterioration of water quality and can produce toxic nitrite, the nitrate constituted of great threatens to human health and eco-systematic safety. Among most well-known biotechnology to remove nitrate, the integrated heterotrophic and autotrophic denitrification (IHAD) process is promising, especially for the organic-limited polluted water. In this work, the IHAD coupled manganese oxidation (IHAD-MnO) process was developed by using Pseudomonas sp. SZF15 (Gram negative strain, and rod-shaped morphology with 2.3 μm in length) in the glass serum bottles. It was found that limited organic content could accelerate nitrate removal rate, and manganese oxidation efficiency can reach up to 60.08%. To further explain carbon conversion characteristics of the process, pure heterotrophic condition assays were conducted, the results confirmed that inorganic carbon will be generated by organic carbon metabolism in heterotrophic condition, the maximum accumulation content of inorganic carbon was 142.21 mg/L (when the initial organic carbon level was 293 mg-C/L). Subsequently, since the consumption of organic carbon, biogenic inorganic carbon can be further utilized by microorganisms to support autotrophic denitrification (AuDN). Besides, X-ray photoelectron spectroscopy (XPS) was employed to analyze precipitation products produced from the process. The magnified Mn 2p spectra results showed that a typical characteristic peak of manganese dioxide was observed with the intense peak at 641.8 eV and a satellite peak at 653.7 eV, respectively. This showed that Mn(II) was oxidized to manganese dioxide by the process, which may be a functional material with adsorption properties. The process posed a highly efficient and cost effective solution with less carbon consumption and less greenhouse gas emission for sustainable water treatment technologies.

Regulation of CO2 fluxes along gradients of water saturation in irrigation canal sediments

Hydrological intermittency affects sediment biogeochemistry, organic carbon (OC) metabolism and carbon dioxide (CO2) emission but the study of the effects of drying is generally confined to natural ecosystems. Agricultural canals are artificial, widespread elements in irrigated floodplains, and regularly subjected to water level fluctuations. The aim of this study was to quantify the CO2 emissions along water saturation gradients in artificial canals to understand the environmental factors regulating these fluxes. CO2 measurements were performed in five replicated canals within the Po River basin (Northern Italy). In each canal we analysed three sites: (i) a spot with exposed, dry sediments; (ii) a spot with inundated, saturated sediments and (iii) a spot with an intermediate level of saturation. Besides dark CO2 flux measurements, net potential nitrification and denitrification rates were measured as proxies of sediment redox potential and due to their CO2 sink and source role, respectively. We hypothesized a site-specific regulation of CO2 emission, depending on the interplay among water saturation, sediment oxidation and organic matter content. Our results suggest that desiccation stimulates mineralization processes and CO2 fluxes, that were mainly dependant on water and organic matter content and correlated with microbial N transformations. CO2 emissions tended to increase along the considered water saturation gradients, almost tripling rates from inundated, saturated (158.2 ± 24.1 mmol CO2 m−2 days−1) to dry, exposed sediments (416.5 ± 78.9 mmol CO2 m−2 days−1). Results also suggest that net potential nitrification and denitrification allow tracing the effects of drying on N microbial communities involved in CO2 fluxes. Net potential nitrification rates produce little effects on CO2 fluxes, but is a good proxy of oxygen (O2) availability, whereas potential denitrification may be responsible for variable fractions (up to 100%) of CO2 production, in wetter sediments.

Characteristics of organic carbon metabolism and bioremediation of petroleum-contaminated soil by a mesophilic aerobic biopile system

An innovative mesophilic aerobic biopile technology was explored to improve the bioremediation efficiency of petroleum-contaminated soil. Under the suitable soil conditions (C:N:P at 100:5:1 and soil moisture content at 18%), the soil pH was hold in the range of 7.4 to 6.8 throughout the bioremediation process, the mesophilic (30 °C-40 °C) and forced aeration (3 h-on/1 h-off) conditions were the critical factors to enhancing petroleum biodegradation. The consumption of bioavailable organic carbon (BAC) which was one of the most important factors regulating microbial metabolism, was positively related (R2 = 0.85, 40 °C) with the rate of petroleum removal. The 50% threshold of BAC could be regarded as the signal for supplementing the soil nutrients in the mesophilic aerobic biopiles to favor petroleum removal. The optimal conditions (40 °C, 3 h-on/1 h-off) maximized the utilization of BAC, promoted the petroleum degradation, and remained the microbial abundance and community composition stable to the greatest extent. In addition, the accumulation of aliphatic acids affected the microbial activity, which limited the efficiency of petroleum degradation to a certain extent. Jointly considering the energy consumption, time cost and soil conditions maintenance, a cost-effective biopile technology was obtained by temperature and aeration regulation and BAC supplementation, which could be applied to engineering application.

The combination of biochar and plant roots improves soil bacterial adaptation to PAH stress: Insights from soil enzymes, microbiome, and metabolome

Polycyclic aromatic hydrocarbon (PAH) contamination in agricultural soils poses serious stress to the soil microbiome. With the broad application of biochar, however, the co-effects of biochar and plant roots on the bacterial responses to PAH stress remain unclear. Here, the effects of biochar and the rhizosphere on bacterial community structure and functions were analyzed by coupling enzyme activity tests, high-throughput sequencing, and soil metabolomics. The contents of available nutrients and dissolved organic carbon, enzyme activities, and carbon metabolism functions were improved by biochar and plant roots. With the combined effects of biochar and plant roots, sucrose and starch metabolism was mainly impacted, and the soil metabolite diversity decreased. There was a strong co-occurrence network among soil properties, bacterial members, and metabolites in the biochar-amended and rhizosphere soils, favoring bacterial resistance to PAH stress, and consequently, PAH removal. In light of the above results, we suggest that biochar application can efficiently improve bacterial functions in rhizosphere soil, and our results facilitate the development of in situ remediation programs in soil contaminated with PAHs.

Shifts in the Bacterial Population and Ecosystem Functions in Response to Vegetation in the Yellow River Delta Wetlands.

Vegetation represents probably the most crucial step for the ecosystem functions of wetlands, but it is unclear how microbial populations and functions shift along with vegetation. In this study, we found that the richness and diversity of soil bacteria increased with vegetation levels and that the community composition was distinctly shifted from bare to vegetative places. The bare land displayed an extremely high abundance of Cyanobacteria as a monospecies genus, while a Gemmatimonadetes genus was predominant as multiple species in all the vegetative wetlands, suggesting their important ecosystem functions and potential mechanisms. Expression of the genes related to photosynthesis was enriched exclusively in bare land. Genes involved in biological organic carbon metabolism and the cycling of main elements (C, N, S, and P) were highly expressed in vegetative wetlands and were mostly included in the metagenome-assembled genome (MAG) of Gemmatimonadetes Some compounds identified from soil metabolomic results also corresponded to pathways involving these key active genes. Cyanobacteria is thus responsible for the carbon sink in early infertile wetlands, and Gemmatimonadetes plays a crucial role in ecosystem functions in vegetative wetlands. Our results highlight that the soil microbial populations execute ecosystem functions for wetlands and that vegetation is the determinant for the population and functional shifts in the coastal estuarine wetland of the Yellow River Delta.IMPORTANCE Vegetation probably represents the most crucial step for the ecosystem functions of wetlands, but it is unclear how microbial populations and functions shift in pace with the colonization and succession of vegetation. In this study, we found that a Cyanobacteria monospecies genus and a Gemmatimonadetes multispecies genus are fastidiously predominant in the bare and vegetative wetlands of the Yellow River Delta, respectively. Consistently, photosynthesis genes were enriched exclusively in bare land, while genes involved in biological organic carbon metabolism and the cycling of main elements were highly expressed in vegetative wetlands, were mostly included in the MAG of Gemmatimonadetes, and were consistent with soil metabolomic results. Our results provide insight into the adaptive succession of predominant bacterial species and their ecosystem functions in response to the presence of vegetation.

Effects of inorganic carbon and light on acetate assimilation by Nannochloropsis oceanica (Eustigmatophyceae) in mixotrophic cultivation

ABSTRACT Microalgae are capable of accumulating biomass and high value-added products in mixotrophic culture. Carbon sources and light intensity have significant impacts on mixotrophic algal growth and metabolites accumulation. To investigate the underlying mechanism of interaction between metabolism of inorganic carbon and organic carbon, growth of Nannochloropsis oceanica with two different carbon sources (organic sodium acetate and inorganic sodium bicarbonate) and under three different light conditions (low, medium and high) was examined. A combination of sodium acetate and sodium bicarbonate significantly enhanced algal growth with higher acetate assimilation, when compared with single carbon sources. With increasing light intensity from low to high, the algal growth rates decreased in both autotrophic and mixotrophic cultures. Proteome and 13C metabolic flux results showed that acetate utilization via the glyoxylate (GOX) cycle was enhanced, and both the tricarboxylic acid (TCA) cycle and putative C4 pathway were stimulated in the presence of sodium acetate and sodium bicarbonate. These data suggest that sodium bicarbonate could facilitate acetate assimilation and enhance the putative C4 pathway, GOX cycle and TCA cycle in N. oceanica under mixotrophic culture conditions.

PH control and microbial community analysis with HCl or CO2 addition in H2-based autotrophic denitrification

H2-based autotrophic denitrification is promising to remove nitrate from water or wastewater lacking organic carbon sources, and pH is one of its most important process parameters. HCl and CO2 addition are known as adequate pH control methods for practical purposes. However, because of H2, added CO2 may participate in microbial metabolisms and affect denitrification mechanisms. Here, a combined micro-electrolysis and autotrophic denitrification (CEAD) reactor, in which H2 is generated based on galvanic-cell reactions between zero-valent iron and carbon, was optimized and continuously operated for 233 days by adding HCl or CO2 to control pH in the range of 7.2–8.2. Microbial communities were compared between the two pH-control methods through high-throughput sequencing of 16S rRNA, nirS, and nirK genes. Under a low COD/N ratio of 0.5 in the influent (with ∼36 mgNO3-–N/L), when adding HCl, the total nitrogen (TN) removal efficiency reached 91.4% ± 0.9% with a 28-h hydraulic retention time (HRT). When adding CO2, the TN removal efficiency was improved to 96.5% ± 1.7% with 24-h HRT. Significant differences of 16S rRNA and nirS genes between the two pH-control stages indicated the variation of microbial communities and nirS-type denitrifiers. With HCl addition, Thiobacillus, unclassified Comamonadaceae, Arenimonas, Limnobacter, and Thermomonas, which were reported previously as likely autotrophic or heterotrophic denitrifiers, were most dominant in the biofilms. With CO2 addition, the biofilms became dominated by Anaerolineaceae and Methylocystaceae (related to organic carbon metabolism), Denitratisoma (likely heterotrophic denitrifier), and uncultured bacteria TK10 and AKYG587. The results suggest that the added CO2 not only contributed to pH control but also participated in microbial metabolisms. This study provides useful insights into microbial mechanisms and further optimization of H2-based autotrophic denitrification in water and wastewater treatment.

Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution.

Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies showed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using cultivation and genomic sequencing, we identified four putative Candidatus Nitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA. Genome analyses indicated highly conserved 16S rRNA gene sequences, but broad metabolic potential including genes for nitrogen, sulfur, hydrogen, and organic carbon metabolism. Genomic predictions suggested that Ca. Nitrotoga can metabolize in low oxygen or anoxic conditions, which may support an expanded environmental niche for Ca. Nitrotoga similar to other NOB. An array of antibiotic and metal resistance genes likely allows Ca. Nitrotoga to withstand environmental pressures in impacted systems. Phylogenetic analyses highlighted a deeply divergent nitrite oxidoreductase alpha subunit (NxrA), suggesting a novel evolutionary trajectory for Ca. Nitrotoga separate from any other NOB and further revealing the complex evolutionary history of nitrite oxidation in the bacterial domain. Ca. Nitrotoga-like 16S rRNA gene sequences were prevalent in globally distributed environments over a range of reported temperatures. This work considerably expands our knowledge of the Ca. Nitrotoga genus and suggests that their contribution to nitrogen cycling should be considered alongside other NOB in wide variety of habitats.

Taking the metabolic pulse of the world's coral reefs.

Worldwide, coral reef ecosystems are experiencing increasing pressure from a variety of anthropogenic perturbations including ocean warming and acidification, increased sedimentation, eutrophication, and overfishing, which could shift reefs to a condition of net calcium carbonate (CaCO3) dissolution and erosion. Herein, we determine the net calcification potential and the relative balance of net organic carbon metabolism (net community production; NCP) and net inorganic carbon metabolism (net community calcification; NCC) within 23 coral reef locations across the globe. In light of these results, we consider the suitability of using these two metrics developed from total alkalinity (TA) and dissolved inorganic carbon (DIC) measurements collected on different spatiotemporal scales to monitor coral reef biogeochemistry under anthropogenic change. All reefs in this study were net calcifying for the majority of observations as inferred from alkalinity depletion relative to offshore, although occasional observations of net dissolution occurred at most locations. However, reefs with lower net calcification potential (i.e., lower TA depletion) could shift towards net dissolution sooner than reefs with a higher potential. The percent influence of organic carbon fluxes on total changes in dissolved inorganic carbon (DIC) (i.e., NCP compared to the sum of NCP and NCC) ranged from 32% to 88% and reflected inherent biogeochemical differences between reefs. Reefs with the largest relative percentage of NCP experienced the largest variability in seawater pH for a given change in DIC, which is directly related to the reefs ability to elevate or suppress local pH relative to the open ocean. This work highlights the value of measuring coral reef carbonate chemistry when evaluating their susceptibility to ongoing global environmental change and offers a baseline from which to guide future conservation efforts aimed at preserving these valuable ecosystems.