Impact of elevated atmospheric CO2 on soil bacteria community in a grazed pasture after 12-year enrichment

This study was designed to compare soil bacterial communities under ambient (aCO2) and elevated (eCO2) carbon dioxide after 12 years of enrichment using Free Air Carbon Dioxide Enrichment (FACE) in a grazed grassland. Grazing animals can have profound effects on nutrient cycling through the return of nutrient in excreta and by their influence on plant community composition through diet selection. The abundance and composition of bacterial communities were evaluated by real-time quantitative Polymerase Chain Reaction (qPCR) and pyrosequencing based on the analysis of bacterial 16S rRNA genes. The results showed the overall bacterial community structure was not altered by the eCO2 treatment despite the substantial changes in soil functions, pools and fluxes under eCO2 documented at this site in previous studies. The dominant phyla in both treatments were Actinobacteria, Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes, accounting for 87% of the total microbial 16S rRNA sequence reads. At the phylum level, Planctomycetes and Bacteria incertae sedis increased and BRC, Cyanobateria and TM7 decreased significantly at eCO2. Most changes were observed at lower taxonomic levels where the abundance of 30 of the 200 most abundant OTUs were responsive to eCO2 however these changes were not sufficient to differentiate the overall communities. It remains uncertain whether these changes in the lower order taxa could be responsible for the observed changes in soil properties. These first data for a grazed ecosystem are broadly consistent with those froma range of other ecosystems where CO2 effects are confined to relatively few taxa

Data_Sheet_1_Rice straw increases microbial nitrogen fixation, bacterial and nifH genes abundance with the change of land use types.docx

Soil microorganisms play an important role in soil ecosystems as the main decomposers of carbon and nitrogen. They have an indispensable impact on soil health, and any alterations in the levels of organic carbon and inorganic nitrogen can significantly affect soil chemical properties and microbial community composition. Previous studies have focused on the effects of carbon and nitrogen addition on a single type of soil, but the response of soil microorganisms to varying carbon and nitrogen inputs under different land soil use types have been relatively understudied, leaving a gap in our understanding of the key influencing factors. To address this gap, we conducted a study in the tropical regions of Hainan province, focusing on four distinct land use types: natural forest soil (NS), healthy banana soil (HS), diseased banana garden soil (DS), and paddy soil (PS). Within each of these environments, we implemented five treatments: CK, RS (rice straw), RSN (rice straw and NH4NO3), RR (rice root), and RRN (rice root and NH4NO3). Our aim was to investigate how soil bacteria response to changes in carbon and nitrogen inputs, and to assess their potential for biological nitrogen fixation. The results showed that the addition of rice straw increased the absorption and utilization of nitrate nitrogen by microorganisms. The addition of rice roots (RR) did not increase the absorption capacity of inorganic nitrogen by microorganisms, but increased the content of poorly soluble organic carbon. Most importantly, the addition of rice straw increased microbial respiration and the utilization efficiency of N2 by microorganisms, and the further addition of ammonium nitrate increased microbial respiration intensity. With the change of soil type, the rice straw increases microbial nitrogen fixation, bacterial and nifH genes abundance. Meanwhile, microbial respiration intensity is an important factor influencing the differences in the structure of bacterial communities. The addition of inorganic nitrogen resulted in ammonium nitrogen accumulation, reduced microbial richness and diversity, consequently diminishing the soil microorganisms to resist the environment. Therefore, we believe that with the change of soil types, corresponding soil nutrient retention strategies should be devised and incorporated while reducing the application of ammonium nitrogen, thus ensuring healthy soil development.</p

Data_Sheet_1_Methanotrophy Alleviates Nitrogen Constraint of Carbon Turnover by Rice Root-Associated Microbiomes.docx

The bioavailability of nitrogen constrains primary productivity, and ecosystem stoichiometry implies stimulation of N2 fixation in association with carbon sequestration in hotspots such as paddy soils. In this study, we show that N2 fixation was triggered by methane oxidation and the methanotrophs serve as microbial engines driving the turnover of carbon and nitrogen in rice roots. 15N2-stable isotope probing showed that N2-fixing activity was stimulated 160-fold by CH4 oxidation from 0.27 to 43.3 μmol N g–1 dry weight root biomass, and approximately 42.5% of the fixed N existed in the form of 15N-NH4+ through microbial mineralization. Nitrate amendment almost completely abolished N2 fixation. Ecophysiology flux measurement indicated that methane oxidation-induced N2 fixation contributed only 1.9% of total nitrogen, whereas methanotrophy-primed mineralization accounted for 21.7% of total nitrogen to facilitate root carbon turnover. DNA-based stable isotope probing further indicated that gammaproteobacterial Methylomonas-like methanotrophs dominated N2 fixation in CH4-consuming roots, whereas nitrate addition resulted in the shift of the active population to alphaproteobacterial Methylocystis-like methanotrophs. Co-occurring pattern analysis of active microbial community further suggested that a number of keystone taxa could have played a major role in nitrogen acquisition through root decomposition and N2 fixation to facilitate nutrient cycling while maintaining soil productivity. This study thus highlights the importance of root-associated methanotrophs as both biofilters of greenhouse gas methane and microbial engines of bioavailable nitrogen for rice growth.</p

Image_5_Methanotrophs Contribute to Nitrogen Fixation in Emergent Macrophytes.JPEG

Root-associated aerobic methanotroph plays an important role in reducing methane emissions from wetlands. In this study, we examined the activity of methane-dependent nitrogen fixation and active nitrogen-fixing bacterial communities on the roots of Typha angustifolia and Scirpus triqueter using a 15N-N2 feeding experiment and a cDNA-based clone library sequence of the nifH gene, respectively. A 15N-N2 feeding experiment showed that the N2 fixation rate of S. triqueter (1.74 μmol h–1 g–1 dry weight) was significantly higther than that of T. angustifolia (0.48 μmol h–1 g–1 dry weight). The presence of CH4 significantly increased the incorporation of 15N-labeled N2 into the roots of both plants, and the rate of CH4-dependent N2 fixation of S. triqueter (5.6 μmol h–1 g–1 dry weight) was fivefold higher than that of T. angustifolia (0.94 μmol h–1 g–1 dry weight). The active root-associated diazotrophic communities differed between the plant species. Diazotrophic Methylosinus of the Methylocystaceae was dominant in S. triqueter, while Rhizobium of the Rhizobiaceae was dominant in T. angustifolia. However, there were no significant differences in the copy numbers of nifH between plant species. These results suggest that N2 fixation was enhanced by the oxidation of CH4 in the roots of macrophytes grown in natural wetlands and that root-associated Methylocystacea, including Methylosinus, contribute to CH4 oxidation-dependent N2 fixation.</p

Image_1_Methanotrophs Contribute to Nitrogen Fixation in Emergent Macrophytes.JPEG

Root-associated aerobic methanotroph plays an important role in reducing methane emissions from wetlands. In this study, we examined the activity of methane-dependent nitrogen fixation and active nitrogen-fixing bacterial communities on the roots of Typha angustifolia and Scirpus triqueter using a 15N-N2 feeding experiment and a cDNA-based clone library sequence of the nifH gene, respectively. A 15N-N2 feeding experiment showed that the N2 fixation rate of S. triqueter (1.74 μmol h–1 g–1 dry weight) was significantly higther than that of T. angustifolia (0.48 μmol h–1 g–1 dry weight). The presence of CH4 significantly increased the incorporation of 15N-labeled N2 into the roots of both plants, and the rate of CH4-dependent N2 fixation of S. triqueter (5.6 μmol h–1 g–1 dry weight) was fivefold higher than that of T. angustifolia (0.94 μmol h–1 g–1 dry weight). The active root-associated diazotrophic communities differed between the plant species. Diazotrophic Methylosinus of the Methylocystaceae was dominant in S. triqueter, while Rhizobium of the Rhizobiaceae was dominant in T. angustifolia. However, there were no significant differences in the copy numbers of nifH between plant species. These results suggest that N2 fixation was enhanced by the oxidation of CH4 in the roots of macrophytes grown in natural wetlands and that root-associated Methylocystacea, including Methylosinus, contribute to CH4 oxidation-dependent N2 fixation.</p

Image_3_Methanotrophs Contribute to Nitrogen Fixation in Emergent Macrophytes.JPEG

Root-associated aerobic methanotroph plays an important role in reducing methane emissions from wetlands. In this study, we examined the activity of methane-dependent nitrogen fixation and active nitrogen-fixing bacterial communities on the roots of Typha angustifolia and Scirpus triqueter using a 15N-N2 feeding experiment and a cDNA-based clone library sequence of the nifH gene, respectively. A 15N-N2 feeding experiment showed that the N2 fixation rate of S. triqueter (1.74 μmol h–1 g–1 dry weight) was significantly higther than that of T. angustifolia (0.48 μmol h–1 g–1 dry weight). The presence of CH4 significantly increased the incorporation of 15N-labeled N2 into the roots of both plants, and the rate of CH4-dependent N2 fixation of S. triqueter (5.6 μmol h–1 g–1 dry weight) was fivefold higher than that of T. angustifolia (0.94 μmol h–1 g–1 dry weight). The active root-associated diazotrophic communities differed between the plant species. Diazotrophic Methylosinus of the Methylocystaceae was dominant in S. triqueter, while Rhizobium of the Rhizobiaceae was dominant in T. angustifolia. However, there were no significant differences in the copy numbers of nifH between plant species. These results suggest that N2 fixation was enhanced by the oxidation of CH4 in the roots of macrophytes grown in natural wetlands and that root-associated Methylocystacea, including Methylosinus, contribute to CH4 oxidation-dependent N2 fixation.</p

Image_2_Methanotrophs Contribute to Nitrogen Fixation in Emergent Macrophytes.JPEG

Root-associated aerobic methanotroph plays an important role in reducing methane emissions from wetlands. In this study, we examined the activity of methane-dependent nitrogen fixation and active nitrogen-fixing bacterial communities on the roots of Typha angustifolia and Scirpus triqueter using a 15N-N2 feeding experiment and a cDNA-based clone library sequence of the nifH gene, respectively. A 15N-N2 feeding experiment showed that the N2 fixation rate of S. triqueter (1.74 μmol h–1 g–1 dry weight) was significantly higther than that of T. angustifolia (0.48 μmol h–1 g–1 dry weight). The presence of CH4 significantly increased the incorporation of 15N-labeled N2 into the roots of both plants, and the rate of CH4-dependent N2 fixation of S. triqueter (5.6 μmol h–1 g–1 dry weight) was fivefold higher than that of T. angustifolia (0.94 μmol h–1 g–1 dry weight). The active root-associated diazotrophic communities differed between the plant species. Diazotrophic Methylosinus of the Methylocystaceae was dominant in S. triqueter, while Rhizobium of the Rhizobiaceae was dominant in T. angustifolia. However, there were no significant differences in the copy numbers of nifH between plant species. These results suggest that N2 fixation was enhanced by the oxidation of CH4 in the roots of macrophytes grown in natural wetlands and that root-associated Methylocystacea, including Methylosinus, contribute to CH4 oxidation-dependent N2 fixation.</p

Image_4_Methanotrophs Contribute to Nitrogen Fixation in Emergent Macrophytes.JPEG

Root-associated aerobic methanotroph plays an important role in reducing methane emissions from wetlands. In this study, we examined the activity of methane-dependent nitrogen fixation and active nitrogen-fixing bacterial communities on the roots of Typha angustifolia and Scirpus triqueter using a 15N-N2 feeding experiment and a cDNA-based clone library sequence of the nifH gene, respectively. A 15N-N2 feeding experiment showed that the N2 fixation rate of S. triqueter (1.74 μmol h–1 g–1 dry weight) was significantly higther than that of T. angustifolia (0.48 μmol h–1 g–1 dry weight). The presence of CH4 significantly increased the incorporation of 15N-labeled N2 into the roots of both plants, and the rate of CH4-dependent N2 fixation of S. triqueter (5.6 μmol h–1 g–1 dry weight) was fivefold higher than that of T. angustifolia (0.94 μmol h–1 g–1 dry weight). The active root-associated diazotrophic communities differed between the plant species. Diazotrophic Methylosinus of the Methylocystaceae was dominant in S. triqueter, while Rhizobium of the Rhizobiaceae was dominant in T. angustifolia. However, there were no significant differences in the copy numbers of nifH between plant species. These results suggest that N2 fixation was enhanced by the oxidation of CH4 in the roots of macrophytes grown in natural wetlands and that root-associated Methylocystacea, including Methylosinus, contribute to CH4 oxidation-dependent N2 fixation.</p

Image_6_Methanotrophs Contribute to Nitrogen Fixation in Emergent Macrophytes.JPEG

Root-associated aerobic methanotroph plays an important role in reducing methane emissions from wetlands. In this study, we examined the activity of methane-dependent nitrogen fixation and active nitrogen-fixing bacterial communities on the roots of Typha angustifolia and Scirpus triqueter using a 15N-N2 feeding experiment and a cDNA-based clone library sequence of the nifH gene, respectively. A 15N-N2 feeding experiment showed that the N2 fixation rate of S. triqueter (1.74 μmol h–1 g–1 dry weight) was significantly higther than that of T. angustifolia (0.48 μmol h–1 g–1 dry weight). The presence of CH4 significantly increased the incorporation of 15N-labeled N2 into the roots of both plants, and the rate of CH4-dependent N2 fixation of S. triqueter (5.6 μmol h–1 g–1 dry weight) was fivefold higher than that of T. angustifolia (0.94 μmol h–1 g–1 dry weight). The active root-associated diazotrophic communities differed between the plant species. Diazotrophic Methylosinus of the Methylocystaceae was dominant in S. triqueter, while Rhizobium of the Rhizobiaceae was dominant in T. angustifolia. However, there were no significant differences in the copy numbers of nifH between plant species. These results suggest that N2 fixation was enhanced by the oxidation of CH4 in the roots of macrophytes grown in natural wetlands and that root-associated Methylocystacea, including Methylosinus, contribute to CH4 oxidation-dependent N2 fixation.</p

Syntrophy of bacteria and archaea in the anaerobic catabolism of hydrocarbon contaminants

The extensive use of organic chemicals has resulted in the widespread distribution of hydrocarbon contaminants (HCs) in many ecosystems on a global scale. Many subterranean ecosystems can rapidly become anaerobic or even methanogenic following hydrocarbon contamination. Bacteria and archaea dominate communities in such systems and mediate the syntrophic processes that transform HCs into methane (CH4). The resulting CH4 is oxidized by anaerobic bacteria and archaea, either jointly or individually, in the presence of electron acceptors (e.g., sulfate, nitrate, nitrite, manganese, or ferric iron), a process that reduces CH4 emissions and, as a result, contributes to climate change mitigation. Although the possibility of the syntrophy of bacteria and archaea in the anaerobic transformation of HCs and methane oxidation is widely established, the specific pathways and syntrophic taxa involved are poorly understood. This paper reviews the syntrophy of bacteria and archaea in anaerobic HC degradation, with a focus on methanogenic processes. In addition, we discuss the role of bacteria and archaea in the anaerobic oxidation of methane (AOM) and its environmental significance. Given that much of the biotransformation of HCs driven by methanogenic and methanotrophic processes remains unknown, we propose a way forward to discover novel syntrophic partners and metabolic pathways in such anoxic systems.</p