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.

Long-term fertilization suppresses rice pathogens by microbial volatile compounds.

Microbial volatile organic compounds (VOCs) can suppress plant pathogens. Although fertilization strongly affects soil microbial communities, the influence of fertilization on microbial VOC-mediated suppression of pathogens has not been elucidated. Soil was sampled from a paddy field that had been subjected to the following treatments for 30 years: a no-fertilizer control, mineral fertilization (NPK), NPK combined with rice straw (NPK + S), NPK combined with chicken manure (70% NPK + 30% M). Then, within a laboratory experiment, pathogens were exposed to VOCs without physical contact to assess the impact of VOCs emitted from paddy soils on in vitro growth of the fungal rice pathogens: Pyricularia oryzae and Rhizoctonia solani. The VOCs emitted from soil reduced the mycelial biomass of P. oryzae and R. solani by 36-51% and 10-30%, respectively, compared to that of the control (no soil; no VOCs emission). Overall, the highest suppression of P. oryzae and R. solani was in the NPK and NPK + S soils, which emitted more quinones, phenols, and low alcohols than NPK + M soils. The abundances of quinones and phenols in the soil air were maximal in the NPK-fertilized soil because the low ratio of dissolved organic carbon and Olsen-P increased the population of key species such as Acidobacteriae, Anaerolineae, and Entorrhizomycetes. The abundance of alcohols was minimum in the NPK + S fertilized soil because the high SOC content decreased the population of Sordariomycetes. In conclusion, mineral fertilization affects bacterial and fungal VOC emissions, thereby suppressing the growth of R. solani and P. oryzae.

Temperature sensitivity of anaerobic methane oxidation versus methanogenesis in paddy soil: Implications for the CH4 balance under global warming.

The global methane (CH4 ) budget is based on a sensitive balance between methanogenesis and CH4 oxidation (aerobic and anaerobic). The response of these processes to climate warming, however, is not quantified. This largely reflects our lack of knowledge about the temperature sensitivity (Q10 ) of the anaerobic oxidation of CH4 (AOM)-a ubiquitous process in soils. Based on a 13 CH4 labeling experiment, we determined the rate, Q10 and activation energy of AOM and of methanogenesis in a paddy soil at three temperatures (5, 20, 35°C). The rates of AOM and of methanogenesis increased exponentially with temperature, whereby the AOM rate was significantly lower than methanogenesis. Both the activation energy and Q10 of AOM dropped significantly from 5-20 to 20-35°C, indicating that AOM is a highly temperature-dependent microbial process. Nonetheless, the Q10 of AOM and of methanogenesis were similar at 5-35°C, implying a comparable temperature dependence of AOM and methanogenesis in paddy soil. The continuous increase of AOM Q10 over the 28-day experiment reflects the successive utilization of electron acceptors according to their thermodynamic efficiency. The basic constant for Q10 of AOM was calculated to be 0.1 units for each 3.2 kJ mol-1 increase of activation energy. We estimate the AOM in paddy soils to consume 2.2~5.5 Tg CH4 per year on a global scale. Considering these results in conjunction with literature data, the terrestrial AOM in total consumes ~30% of overall CH4 production. Our data corroborate a similar Q10 of AOM and methanogenesis. As the rate of AOM in paddy soils is lower than methanogenesis, however, it will not fully compensate for an increased methane production under climate warming.

Visualization and quantification of carbon "rusty sink" by rice root iron plaque: Mechanisms, functions, and global implications.

Paddies contain 78% higher organic carbon (C) stocks than adjacent upland soils, and iron (Fe) plaque formation on rice roots is one of the mechanisms that traps C. The process sequence, extent and global relevance of this C stabilization mechanism under oxic/anoxic conditions remains unclear. We quantified and localized the contribution of Fe plaque to organic matter stabilization in a microoxic area (rice rhizosphere) and evaluated roles of this C trap for global C sequestration in paddy soils. Visualization and localization of pH by imaging with planar optodes, enzyme activities by zymography, and root exudation by 14 C imaging, as well as upscale modeling enabled linkage of three groups of rhizosphere processes that are responsible for C stabilization from the micro- (root) to the macro- (ecosystem) levels. The 14 C activity in soil (reflecting stabilization of rhizodeposits) with Fe2+ addition was 1.4-1.5 times higher than that in the control and phosphate addition soils. Perfect co-localization of the hotspots of ß-glucosidase activity (by zymography) with root exudation (14 C) showed that labile C and high enzyme activities were localized within Fe plaques. Fe2+ addition to soil and its microbial oxidation to Fe3+ by radial oxygen release from rice roots increased Fe plaque (Fe3+ ) formation by 1.7-2.5 times. The C amounts trapped by Fe plaque increased by 1.1 times after Fe2+ addition. Therefore, Fe plaque formed from amorphous and complex Fe (oxyhydr)oxides on the root surface act as a "rusty sink" for organic matter. Considering the area of coverage of paddy soils globally, upscaling by model revealed the radial oxygen loss from roots and bacterial Fe oxidation may trap up to 130 Mg C in Fe plaques per rice season. This represents an important annual surplus of new and stable C to the existing C pool under long-term rice cropping.

Rapid, sensitive analysis method for determining the nitrogen stable isotope ratio of total free amino acids in soil.

RATIONALE: The amino acid-nitrogen (AA-N) isotope analysis of naturally abundant or isotope-labeled samples is indispensable for tracing nitrogen transfer in soil nitrogen biogeochemical cycling processes. Despite the usefulness of AA-N isotope analysis, the preparation methods are complex and time-consuming, and necessitate the use of toxic reagents. METHODS: We present an improved, rapid method for AA-N isotope analysis with high precision. At a high pH, AA-N was released and oxidized to N2 O using ClO- under vacuum. Additionally, purge-and-trap isotope ratio mass spectrometry was used to analyze N2 O. Moreover, we investigated the effect of various factors on the N2 O conversion process with glycine and applied the results to seven representative single-N AAs (alanine, serine, cysteine, aspartic acid, glutamic acid, leucine, and phenylalanine) and five poly-N AAs (lysine, arginine, histidine, tryptophan, and asparagine), as well as side-chain analogs, blank reagent, and other N forms. RESULTS: The concentration of ClO- and the pH were determined to be crucial factors for achieving desirable AA-N to N2 O conversion efficiencies. Glycine-N had the highest N2 O yield of 70%, with isotopic results consistent with those of the reference values at a high precision (within 0.5‰ for natural abundance and 0.01 atom% for 15 N-enrichment) at the nanomolar N level. Additionally, the α-NH2 AAs were labile, and the single-N AAs were more easily converted to N2 O than poly-N AAs. With the exception of γ-aminobutyric acid, the N2 O conversion efficiencies of the side-chain N analogs were very low (below 5%). This method was also applicable to the 15 N analysis of the total free AAs in complex soil samples without interference from analytical blanks and other forms of N. CONCLUSIONS: Our method is highly selective for the α-NH2 groups of an amino acid, and the oxidation of the side chain is difficult. In addition, the method is sensitive, rapid, and convenient, and does not require toxic reagents.

Characterization of the belowground microbial community and co-occurrence networks of tobacco plants infected with bacterial wilt disease.

Characterizing the microbial communities associated with soil-borne disease incidence is a key approach in understanding the potential role of microbes in protecting crops from pathogens. In this study, we compared the soil properties and microbial composition of the rhizosphere soil and roots of healthy and bacterial wilt-infected tobacco plants to assess their potential influence on plant health. Our results revealed that the relative abundance of pathogens was higher in diseased plants than in healthy plants. Moreover, compared with healthy plants, there was a significantly higher microbial alpha diversity in the roots and rhizosphere soil of diseased plants. In addition, we detected a lower abundance of certain plant microbiota, including species in the genera Penicillium, Trichoderma, and Burkholderia in the rhizosphere of diseased plants, which were found to be significantly negatively associated with the relative abundance of Ralstonia. Indeed, compared with healthy plants, the co-occurrence networks of diseased plants included a larger number of associations linked to plant health. Furthermore, structural equation modeling revealed that these specific microbes were correlated with disease suppression, thereby implying that they may play important roles in maintaining plant health. In conclusion, our findings provide important insights into the relationships between soil-borne disease incidence and changes in the belowground microbial community. These findings will serve as a basis for further research investigating the use of specific plant-associated genera to inhibit soil-borne diseases.

Metagenomic and 14 C tracing evidence for autotrophic microbial CO2 fixation in paddy soils.

Autotrophic carbon dioxide (CO2 ) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with 14 C-labelling to investigate all known autotrophic pathways and CO2 assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%-82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of 14 C-CO2 are assimilated into SOC (74.3-175.8 mg 14 C kg-1 ) and microbial biomass (5.2-24.1 mg 14 C kg-1 ) after 45 days incubation, where more than 70% of 14 C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool.

Contrasting pathways of carbon sequestration in paddy and upland soils.

Paddy soils make up the largest anthropogenic wetlands on earth, and are characterized by a prominent potential for organic carbon (C) sequestration. By quantifying the plant- and microbial-derived C in soils across four climate zones, we identified that organic C accrual is achieved via contrasting pathways in paddy and upland soils. Paddies are 39%-127% more efficient in soil organic C (SOC) sequestration than their adjacent upland counterparts, with greater differences in warmer than cooler climates. Upland soils are more replenished by microbial-derived C, whereas paddy soils are enriched with a greater proportion of plant-derived C, because of the retarded microbial decomposition under anaerobic conditions induced by the flooding of paddies. Under both land-use types, the maximal contribution of plant residues to SOC is at intermediate mean annual temperature (15-20°C), neutral soil (pH~7.3), and low clay/sand ratio. By contrast, high temperature (~24°C), low soil pH (~5), and large clay/sand ratio are favorable for strengthening the contribution of microbial necromass. The greater contribution of microbial necromass to SOC in waterlogged paddies in warmer climates is likely due to the fast anabolism from bacteria, whereas fungi are unlikely to be involved as they are aerobic. In the scenario of land-use conversion from paddy to upland, a total of 504 Tg C may be lost as CO2 from paddy soils (0-15 cm) solely in eastern China, with 90% released from the less protected plant-derived C. Hence, preserving paddy systems and other anthropogenic wetlands and increasing their C storage through sustainable management are critical for maintaining global soil C stock and mitigating climate change.

Diazotrophic Community Variation Underlies Differences in Nitrogen Fixation Potential in Paddy Soils Across a Climatic Gradient in China.

Biological nitrogen (N2) fixation as a source of new N input into the soil by free-living diazotrophs is important for achieving sustainable rice agriculture. However, the dominant environmental drivers or factors influencing N2 fixation and the functional significance of the diazotroph community structure in paddy soil across a climatic gradient are not yet well understood. Thus, we characterized the diazotroph community and identified the ecological predictors of N2 fixation potential in four different climate zones (mid-temperate, warm-temperate, subtropical, and tropical paddy soils) in eastern China. Comprehensive nifH gene sequencing, functional activity detection, and correlation analysis with environmental factors were estimated. The potential nitrogenase activity (PNA) was highest in warm-temperate regions, where it was 6.2-, 2.9-, and 2.2-fold greater than in the tropical, subtropical, and mid-temperate regions, respectively; nifH gene abundance was significantly higher in warm-temperate and subtropical zones than in the tropical or mid-temperate zones. Diazotroph diversity was significantly higher in the tropical climate zone and significantly lower in the mid-temperate zone. Non-metric multidimensional scaling and canonical correlation analysis indicated that paddy soil diazotroph populations differed significantly among the four climate zones, mainly owing to differences in climate and soil pH. Structural equation models and automatic linear models revealed that climate and nutrients indirectly affected PNA by affecting soil pH and diazotroph community, respectively, while diazotroph community, C/P, and nifH gene abundance directly affected PNA. And C/P ratio, pH, and the diazotroph community structure were the main predictors of PNA in paddy soils. Collectively, the differences in diazotroph community structure have ecological significance, with important implications for the prediction of soil N2-fixing functions under climate change scenarios.

T4-like Phages Reveal the Potential Role of Viruses in Soil Organic Matter Mineralization.

Viruses are the most abundant biological entities in the world, but their ecological functions in soil are virtually unknown. We hypothesized that greater abundance of T4-like phages will increase bacterial death and thereby suppress soil organic carbon (SOC) mineralization. A range of phage and bacterial abundances were established in sterilized soil by reinoculation with 10-3 and 10-6 dilutions of suspensions of unsterilized soil. The total and viable 16S rRNA gene abundance (a universal marker for bacteria) was measured by qPCR to determine bacterial abundance, with propidium monoazide (PMA) preapplication to eliminate DNA from non-viable cells. Abundance of the g23 marker gene was used to quantify T4-like phages. A close negative correlation between g23 abundance and viable 16S rRNA gene abundance was observed. High abundance of g23 led to lower viable ratios for bacteria, which suggested that phages drove microbial necromass production. The CO2 efflux from soil increased with bacterial abundance but decreased with higher abundance of T4-like phages. Elimination of extracellular DNA by PMA strengthened the relationship between CO2 efflux and bacterial abundance, suggesting that SOC mineralization by bacteria is strongly reduced by the T4-like phages. A random forest model revealed that abundance of T4-like phages and the abundance ratio of T4-like phages to bacteria are better predictors of SOC mineralization (measured as CO2 efflux) than bacterial abundance. Our study provides experimental evidence of phages' role in organic matter turnover in soil: they can retard SOC decomposition but accelerate bacterial turnover.

Flooding and straw returning regulates the partitioning of soil phosphorus fractions and phoD-harboring bacterial community in paddy soils.

Flooding and straw returning are effective agricultural practices in promoting phosphorus (P) availability in paddy soils. However, little is known about the effects of these practices and their interaction on the soil P pools and functional microbes responsible for soil P mobilization. Our 4-year paddy field experiment aimed to analyze the responses of soil P fractions and phoD-harboring bacterial communities in a double-rice cropping system to intermittent flooding (IF) and continuous flooding (CF), in plots with (+ S) and without (-S) straw return. Compared to IF, CF significantly increased soil citrate-P and marginally decreased the HCl-P fractions, suggesting that the stable inorganic P pools are transferred to labile inorganic P at lower redox potentials. Compared to the -S treatments, + S treatments significantly increased the labile organic fractions (enzyme-P). Correspondingly, a decreased soil total organic P concentration was observed in + S treatment. Additionally, + S treatment significantly increased the activity of acid phosphomonoesterase and alkaline phosphomonoesterase and the abundance of phoD-harboring bacteria. These results indicated that straw promoted organic P minimization to release orthophosphate. The diversity of the phoD-harboring bacteria and complexity of the co-occurrence network decreased under the CF + S treatment; however, all keystone species of the phoD-harboring bacteria were retained in this oxygen-deficient environment. This study highlights that irrigation regimes mediate the processes of inorganic P mobilization, while straw returns regulate the processes of organic P mineralization. Additionally, flooding could be a more effective agricultural practice than straw returning to promote soil P availability in paddy soils. KEY POINTS: •Soil P pools and phoD-harboring bacteria communities were assessed. •Straw return mainly affects the mineralization of organic P. •Continuous flooding mainly affects the mobilization of inorganic P.

Enrichment of beneficial rhizosphere microbes in Chinese wheat yellow mosaic virus-resistant cultivars.

The microbial community within the root system, the rhizosphere closely connected to the root, and their symbiotic relationship with the host are increasingly seen as possible drivers of natural pathogen resistance. Resistant cultivars have the most effective strategy in controlling the Chinese wheat yellow mosaic disease, but the roles of the root and rhizosphere microbial interactions among different taxonomic levels of resistant cultivars are still unknown. Thus, we aimed to investigate whether these microbial community composition and network characteristics are related to disease resistance and to analyze the belowground plant-associated microflora. Relatively high microbial diversity and stable community structure for the resistant cultivars were detected. Comparison analysis showed that some bacterial phyla were significantly enriched in the wheat root or rhizosphere of the resistant wheat cultivar. Furthermore, the root and rhizosphere of the resistant cultivars greatly recruited many known beneficial bacterial and fungal taxa. In contrast, the relative abundance of potential pathogens was higher for the susceptible cultivar than for the resistant cultivar. Network co-occurrence analysis revealed that a much more complex, more mutually beneficial, and a higher number of bacterial keystone taxa in belowground microbial networks were displayed in the resistant cultivar, which may have been responsible for maintaining the stability and ecological balance of the microbial community. Overall, compared with the susceptible cultivar, the resistant cultivar tends to recruit more potential beneficial microbial groups for plant and rhizosphere microbial community interactions. These findings indicate that beneficial rhizosphere microbiomes for cultivars should be targeted and evaluated using community compositional profiles. KEY POINTS: • Different resistance levels in cultivars affect the rhizosphere microbiome.. • Resistant cultivars tend to recruit more potential beneficial microbial groups. • Bacteria occupy a high proportion and core position in the microflora network.

Long-Read Amplicon Sequencing of Nitric Oxide Dismutase (nod) Genes Reveal Diverse Oxygenic Denitrifiers in Agricultural Soils and Lake Sediments.

Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N2 and O2. So far, the ecological role of these microbes is not well understood. The only available tool for a targeted study of oxygenic denitrifiers is their respective maker gene, nitric oxide dismutase (nod). Here, we established the use of PacBio long-read sequencing of nod gene amplicons to study the diversity and community structure of oxygenic denitrifiers. Two distinct sets of environmental samples, agricultural soil and lake sediment, were investigated as examples. The circular consensus sequences (ca 1.0 kb) obtained covered most substitution characteristic of NO dismutase and allowed for reliable classification of oxygenic denitrifiers. Distinct nod gene pools and community structure were revealed for the different habitats, with most sequence types affiliated to yet unidentified environmental nod lineages. The abundance of nod genes ranged 2.2 × 106-3.2 × 107 gene copies g-1 soil or sediment, accounting for up to 3% of total bacterial 16S rRNA gene counts. This study indicates that nod-gene-targeted long-read sequencing can be a powerful tool for studying the ecology of these novel microbes, and the results also suggest that oxygenic denitrifiers are prevalent and abundant in different terrestrial samples, where they could play an important, but yet overlooked role in nitrogen transformations.

Contrasting patterns and drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests.

Subtropical broadleaved forests play a crucial role in supporting terrestrial ecosystem functions, but little is known about their belowground soil fungal communities despite that they have central functions in C, N, and P cycles. This study investigated the structures and identified the drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests, using high-throughput sequencing and FUNGuild for fungal identification and assignment to the trophic guild. Fungal richness was much higher in the deciduous than in the evergreen forest. Both forests were dominated by Ascomycota and Basidiomycota phyla, but saprophytic fungi were more abundant in the deciduous forest and ectomycorrhizal fungi predominated in the evergreen forest. Fungal communities had strong links to plant and soil properties. Specifically, plant diversity and litter biomass were the main aboveground drivers of fungal diversity and composition in the deciduous forest, while host effects were prominent in the evergreen forest. The belowground factors, i.e., soil pH, water content, and nutrients especially available P, were identified as the primary drivers of soil fungal communities in the broadleaved forests. Co-occurrence network analysis revealed assembly of fungal composition in broadleaved forest soils was non-random. The smaller modularity of the network in the deciduous forest reflects lower resistance to environment changes. Concluding, these results showed that plant community attributes, soil properties, and potential interactions among fungal functional guilds operate jointly on the divergence of soil fungal community assembly in the two broadleaved forest types.

Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil.

Studying shifts in microbial communities under different land use can help in determining the impact of land use on microbial diversity. In this study, we analyzed four different land-use types to determine their bacterial and archaeal diversity and abundance. Three natural ecosystems, that is, wetland (WL), grassland (GL), and forest (FR) soils, and one agricultural soil, that is, tea plantation (TP) soil, were investigated to determine how land use shapes bacterial and archaeal diversity. For this purpose, molecular analyses, such as quantitative polymerase chain reaction (Q-PCR), 16S rRNA gene sequencing, and terminal restriction fragment length polymorphism (T-RFLP), were used. Soil physicochemical properties were determined, and statistical analyses were performed to identify the key factors affecting microbial diversity in these soils. Phylogenetic affiliations determined using the Ribosomal Database Project (RDP) database and T-RFLP revealed that the soils had differing bacterial diversity. WL soil was rich in only Proteobacteria, whereas GR soil was rich in Proteobacteria, followed by Actinobacteria. FR soil had higher abundance of Chloroflexi species than these soils. TP soil was rich in Actinobacteria, followed by Chloroflexi, Acidobacteria, Proteobacteria, and Firmicutes. The archaeal diversity of GL and FR soils was similar in that most of their sequences were closely related to Nitrososphaerales (Thaumarchaeota phylum). In contrast, WL soil, followed by TP soil, had greater archaeal diversity than other soils. Eight different archaeal classes were found in WL soil, and Pacearchaeota class was the richest one. The abundance of bacterial and archaeal 16S rRNA gene copies in WL and GL soils was significantly higher than that in FR and TP soils. Redundancy analysis showed that bacterial diversity was influenced by abiotic factors, e.g., total organic carbon and pH, whereas total nitrogen, pH, and cation exchange capacity (CEC) significantly affected archaeal community composition. Pearson correlation analysis showed that bacterial and archaeal 16S rRNA gene abundance had the highest correlation with clay content (r > 0.905, P < 0.01), followed by total-P, CEC, pH, and silt (%). These results will lead to more comprehensive understanding of how land use affects microbial distribution.

Soil Carbon-Fixation Rates and Associated Bacterial Diversity and Abundance in Three Natural Ecosystems.

CO2 assimilation by autotrophic microbes is an important process in soil carbon cycling, and our understanding of the community composition of autotrophs in natural soils and their role in carbon sequestration of these soils is still limited. Here, we investigated the autotrophic C incorporation in soils from three natural ecosystems, i.e., wetland (WL), grassland (GR), and forest (FO) based on the incorporation of labeled C into the microbial biomass. Microbial assimilation of 14C (14C-MBC) differed among the soils from three ecosystems, accounting for 14.2-20.2% of 14C-labeled soil organic carbon (14C-SOC). We observed a positive correlation between the cbbL (ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit gene) abundance, 14C-SOC level, and 14C-MBC concentration confirming the role of autotrophic bacteria in soil carbon sequestration. Distinct cbbL-bearing bacterial communities were present in each soil type; form IA and form IC RubisCO-bearing bacteria were most abundant in WL, followed by GR soils, with sequences from FO soils exclusively derived from the form IC clade. Phylogenetically, the diversity of CO2-fixing autotrophs and CO oxidizers differed significantly with soil type, whereas cbbL-bearing bacterial communities were similar when assessed using coxL. We demonstrate that local edaphic factors such as pH and salinity affect the C-fixation rate as well as cbbL and coxL gene abundance and diversity. Such insights into the effect of soil type on the autotrophic bacterial capacity and subsequent carbon cycling of natural ecosystems will provide information to enhance the sustainable management of these important natural ecosystems.

Abundance and Diversity of CO2-Assimilating Bacteria and Algae Within Red Agricultural Soils Are Modulated by Changing Management Practice.

Elucidating the biodiversity of CO(2)-assimilating bacterial and algal communities in soils is important for obtaining a mechanistic view of terrestrial carbon sinks operating at global scales. "Red" acidic soils (Orthic Acrisols) cover large geographic areas and are subject to a range of management practices, which may alter the balance between carbon dioxide production and assimilation through changes in microbial CO(2)-assimilating populations. Here, we determined the abundance and diversity of CO(2)-assimilating bacteria and algae in acidic soils using quantitative PCR and terminal restriction fragment length polymorphism (T-RFLP) of the cbbL gene, which encodes the key CO(2) assimilation enzyme (ribulose-1,5-bisphosphate carboxylase/oxygenase) in the Calvin cycle. Within the framework of a long-term experiment (Taoyuan Agro-ecosystem, subtropical China), paddy rice fields were converted in 1995 to four alternative land management regimes: natural forest (NF), paddy rice (PR), maize crops (CL), and tea plantations (TP). In 2012 (17 years after land use transformation), we collected and analyzed the soils from fields under the original and converted land management regimes. Our results indicated that fields under the PR soil management system harbored the greatest abundance of cbbL copies (4.33 × 10(8) copies g(-1) soil). More than a decade after converting PR soils to natural, rotation, and perennial management systems, a decline in both the diversity and abundance of cbbL-harboring bacteria and algae was recorded. The lowest abundance of bacteria (0.98 × 10(8) copies g(-1) soil) and algae (0.23 × 10(6) copies g(-1) soil) was observed for TP soils. When converting PR soil management to alternative management systems (i.e., NF, CL, and TP), soil edaphic factors (soil organic carbon and total nitrogen content) were the major determinants of bacterial autotrophic cbbL gene diversity. In contrast, soil phosphorus concentration was the major regulator of algal cbbL community composition. Our results provide new insights into the diversity, abundance, and modulation of organisms responsible for microbial autotrophic CO(2) fixation in red acidic soils subjected to changing management regimes.

Changes in bacterial CO2 fixation with depth in agricultural soils.

Soils were incubated continuously in an atmosphere of (14)CO2 and the distribution of labeled C into soil organic carbon ((14)C-SOC) was determined at 0-1, 1-5, and 5-17 cm down the profile. Significant amounts of (14)C-SOC were measured in paddy soils with a mean of 1,180.6 ± 105.2 mg kg(-1) at 0-1 cm and 135.3 ± 47.1 mg kg(-1) at 1-5 cm. This accounted for 5.9 ± 0.7% and 0.7 ± 0.2%, respectively, of the total soil organic carbon at these depths. In the upland soils, the mean (14)C-SOC concentrations were 43 times (0-1 cm) and 11 times (1-5 cm) lower, respectively, than those in the paddy soils. The amounts of (14)C incorporated into the microbial biomass (MBC) were also much lower in upland soils (5.0 ± 3.6% and 2.9 ± 1.9% at 0-1 and 1-5 cm, respectively) than in paddy soils (34.1 ± 12.4% and 10.2 ± 2.1% at 0-1 and 1-5 cm, respectively). Similarly, the amount of (14)C incorporated into the dissolved organic carbon (DOC) was considerably higher in paddy soils (26.1 ± 6.9% and 6.9 ± 1.3% at 0-1 and 1-5 cm, respectively) than in upland soils (6.0 ± 2.7% and 4.3 ± 2.2%, respectively). The observation that the majority of the fixed (14)C-SOC, RubisCO activity and cbbL gene abundance were concentrated at 0-1 cm depth and the fact that light is restricted to the top few millimeters of the soil profiles highlighted the importance of phototrophs in CO2 fixation in surface soils. Phylogenetic analysis of the cbbL genes showed that the potential for CO2 fixation was evident throughout the profile and distributed between both photoautotrophic and chemoautotrophic bacteria such as Rhodopseudomonas palustris, Bradyrhizobium japonicum, Rubrivivax gelatinosus and Ralstonia eutropha.

In situ simultaneous measuring method for the determination of key processes of soil organic carbon cycling: Soil microbial respiration using laser spectrometry.

RATIONALE: Soil microbial heterotrophic C-CO2 respiration is important for C cycling. Soil CO2 differentiation and quantification are vital for understanding soil C cycling and CO2 emission mitigation. Presently, soil microbial respiration (SR) quantification models are based on native soil organic matter (SOM) and require consistent monitoring of δ13C and CO2. METHODS: We present a new apparatus for achieving in situ soil static chamber incubation and simultaneous CO2 and δ13C monitoring by cavity ring-down spectroscopy (CRDS) coupled with a soil culture and gas introduction module (SCGIM) with multi-channel. After a meticulous five-point inter-calibration, the repeatability of CO2 and δ13C values by using CRDS-SCGIM were determined, and compared with those obtained using gas chromatography (GC) and isotope ratio mass spectrometry (IRMS), respectively. We examined the method regarding quantifying SR with various concentrations and enrichment of glucose and then applied it to investigate the responses of SR to the addition of different exogenous organic materials (glucose and rice residues) into paddy soils during a 21-day incubation. RESULTS: The CRDS-SCGIM CO2 and δ13C measurements were conducted with high precision (< 1.0 µmol/mol and 1‰, respectively). The optimal sampling interval and the amount added were not exceeded 4 h and 200 mg C/100 g dry soil in a 1 L incubation bottle, respectively; the 13C-enrichment of 3%-7% was appropriate. The total SR rates observed were 0.6-4.2 µL/h/g and the exogenous organic materials induced -49%-28% of priming effects in native SOM mineralisation. CONCLUSIONS: Our results show that CRDS-SCGIM is a method suitable for the quantification of soil microbial CO2 respiration, requiring less extensive lab resources than GC/IRMS.

Intensive N2 fixation accelerates microbial turnover in cropland soils.

Biological nitrogen fixation (BNF) is strongly affected by the carbon (C) and nitrogen (N) stoichiometry in soil and depends on the input of organic C. Due to the high metabolic costs of nitrogenase activity, however, the response of BNF to organic C input and its impact on microbial turnover remain unclear. To address this knowledge gap, we combined 15N2 tracing with high-throughput sequencing by adding glucose or glucose plus mineral N fertilizer for a 12-day incubation in three cropland soils. Glucose addition alone strongly changed the BNF activity (0.76-2.51 mg N kg-1 d-1), while BNF was completely absent after mineral N fertilization. This switch-on of BNF by glucose addition supported equally high rates of microbial growth and organic C mineralization compared with the direct mineral N assimilation by microorganisms. Glucose-induced BNF was predominantly catalyzed by Azotobacter-affiliated free-living diazotrophs (>50 % of the total nifH genes), which increased with diverse nondiazotrophs such as Nitrososphaera, Bacillus and Pseudoxanthomonas. Structural equation models (SEMs) and random forest (RF) analyses consistently revealed that the soil C:N ratio and Azotobacter-affiliated diazotrophic abundances were the key factors affecting glucose-induced BNF. Our findings emphasize the importance of free-living diazotrophs for microbial turnover of organic C in soil.