Effect of plant-self debris on nitrogen removal, transformation and microbial community in mesocosm constructed wetlands planted with Myriophyllum aquaticum.

Aquatic macrophytes debris decomposition could release pollutants and nutrients into the water of constructed wetlands (CWs), but their role in nitrogen removal and transformation remains poorly understood. The present study investigated the effects of plant-self debris on nitrogen removal and microbial communities in mesocosm CWs planted with Myriophyllum aquaticum. During the 68-day operation, the plant debris addition did not change the mean removal efficiency of ammonium (NH4+-N) and total nitrogen (TN) of CWs but showed significant differences over the operation time. The NH4+-N and organic nitrogen released from the plant debris decomposition affected the nitrogen removal. The plant debris decreased the effluent nitrate concentration and N2O emission fluxes of the CWs with the increased abundance of denitrifying bacterial genera, indicating that plant debris decomposition increased the denitrification activities via dissolved organic carbon release. High-throughput sequencing indicated that the plant debris altered the distribution and composition of the microbial community in the sediments. Proteobacteria was the dominant phylum (28-52%), and the relative abundance of denitrifying bacteria genera was significantly higher in the sediments with debris addition (37-40%) than in the non-addition (6.6-7.7%). The present study provided new insights into the role of macrophytes in pollutant removal and the plant management strategy of CWs.

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.

Physiological response and tolerance of Myriophyllum aquaticum to a wide range of ammonium concentrations.

Myriophyllum aquaticum (M. aquaticum) can be used in constructed wetlands (CWs) to effectively purify swine wastewater with high-ammonia nitrogen (NH3-N and NH4+-N) concentrations. However, the understanding of its tolerance mechanism to ammonia nitrogen is limited. The physiological response and tolerance mechanism of M. aquaticum to a wide range of NH4+ concentrations (0-35 mM) were investigated in the present study. The results indicated that M. aquaticum can tolerate NH4+ concentrations of up to 30 mM for 21 days and grow well with high nutrient (N, P) uptake. A suitable concentration of NH4+ for a better growth of M. aquaticum was 0.5-20 mM. The free NH4+ content was no obviously increase at NH4+ concentration below 15 mM, indicated there was no obviously ammonium accumulation. Exogenous NH4+ inhibited K+ absorption and improved Ca2+ absorption, indicating mineral cation could mediate NH4+ homeostasis under NH4+ stress. Moreover, comparison with those in the control group, the activities of glutamine synthetase (GS), glutamate synthetase (GOGAT) in M. aquaticum increased by 52.7%-115% at 1-20 mM NH4+, and superoxide dismutase (SOD) increased by 29.2-143% at 1-35 mM NH4+. This indicated that the high NH4+ tolerance of M. aquaticum was mainly due to the balance of free NH4+ content in tissues, as well as improved nitrogen metabolism and antioxidant system. This could be attributed to the role of the GS-GOGAT cycle and SOD. In conclusion, M. aquaticum, which tolerates high NH4+ concentration and has a high N uptake ability, can be used as a good candidate specie to help develop more efficient management strategies for treating high-NH4+ wastewater in CW systems.

Influence path identification of topography, soil, hydrology and landscape on phosphorus buffering capacity in typical agricultural catchments in central subtropical China.

The catchment phosphorus buffering capacity (PBF) determines the pressure-state-response relationship between anthropogenic P inputs and aquatic ecosystems at a catchment scale, and is affected by biogeochemical, hydrological, and ecological catchment characteristics. However, the complex relationship between these catchment characteristic factors and their impact pathways on PBF remains ambiguous, leading to large uncertainty in balancing agricultural productivity and water conservation via improving BF through management practices. In this study, the short-term buffering index, calculated from net anthropogenic P input and riverine P exports, was used to quantify the spatiotemporal variations in PBF in source agricultural catchments in the Dongting Lake basin. Partial least squares structural equation modeling was used to investigate the relationship between the PBF and the catchment characteristics. The results indicate that catchment PBF was directly determined by soil properties and hydrological conditions, while landscape patterns significantly mediated the effects of topography on soil and hydrology. Considering the pathway preferences of the model, landscape patterns could be the priority for characterizing and regulating PBF. According to a change-point analysis, the probability of PBF weakening increases dramatically when the proportion of farmland (Farm%) > 24.6%, degree of patch interspersion (Contagion index) < 64.5%, and Perimeter-Area Ratio Distribution (PARA) > 348.7. These findings provide new insights into catchment buffering mechanisms and can be used to promote the simultaneous achievement of agricultural production and environmental conservation goals.

Multi-spatial scale effects of multidimensional landscape pattern on stream water nitrogen pollution in a subtropical agricultural watershed.

Multidimensional (coupled land use, soil properties, and topography) landscape effects on stream water nitrogen (N) are complex and scale-dependent. However, studies that identify critical buffer zones that explain large variations in riverine N, and estimate specific thresholds of multidimensional landscape patterns at the class level, result in a sudden changes in riverine N pollution, are still limited. Here, a new multidimensional landscape metric that combined land use, soil properties, and topography effects was applied to various riparian buffer zones and sub-watershed scales, and their relationships to riverine N levels were investigated. We used stream water ammonium-N, nitrate-N, and total-N concentrations datasets, from 2010 to 2017, in the nine subtropical sub-watersheds in China. The results of model selection and model averaging in ordinary least squares regressions, indicated that the riparian buffer zone with widths of 400 m, had more pronounced influence on water NH4-N and TN levels than at other scales. Within the 400 m buffer zone, the key landscape metrics for NH4-N, NO3-N and TN concentrations in stream water were different, and explained up to 43.35%-76.55% (adjusted R2) of the total variation in river N levels. When ENN_MNClass17 below 39-56 m, PDClass8 above 4.63-6.55 n/km2, PLANDClass27 above 23-29%, and CONTIG_MNClass42 below 0.35-0.37% within the 400 m buffer zone, riverine NH4-N and TN would be abruptly increased. This study provided practical ideas for regulation regarding landscape management linked to watershed structure, and identified reference thresholds for multidimensional landscape metrics, which should help reduce riverine N pollution in subtropical China.

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.

Economics- and policy-driven organic carbon input enhancement dominates soil organic carbon accumulation in Chinese croplands.

China's croplands have experienced drastic changes in management practices, such as fertilization, tillage, and residue treatments, since the 1980s. There is an ongoing debate about the impact of these changes on soil organic carbon (SOC) and its implications. Here we report results from an extensive study that provided direct evidence of cropland SOC sequestration in China. Based on the soil sampling locations recorded by the Second National Soil Survey of China in 1980, we collected 4,060 soil samples in 2011 from 58 counties that represent the typical cropping systems across China. Our results showed that across the country, the average SOC stock in the topsoil (0-20 cm) increased from 28.6 Mg C ha-1 in 1980 to 32.9 Mg C ha-1 in 2011, representing a net increase of 140 kg C ha-1 year-1 However, the SOC change differed among the major agricultural regions: SOC increased in all major agronomic regions except in Northeast China. The SOC sequestration was largely attributed to increased organic inputs driven by economics and policy: while higher root biomass resulting from enhanced crop productivity by chemical fertilizers predominated before 2000, higher residue inputs following the large-scale implementation of crop straw/stover return policy took over thereafter. The SOC change was negatively related to N inputs in East China, suggesting that the excessive N inputs, plus the shallowness of plow layers, may constrain the future C sequestration in Chinese croplands. Our results indicate that cropland SOC sequestration can be achieved through effectively manipulating economic and policy incentives to farmers.

Nitrogen removal characteristics of a novel heterotrophic nitrification and aerobic denitrification bacteria, Alcaligenes faecalis strain WT14.

Alcaligenes faecalis strain WT14 is heterotrophic nitrification and aerobic denitrification bacterium, newly isolated from a constructed wetland, and its feasibility in nitrogen removal was investigated. The result showed sodium citrate was more readily utilized by WT14 as a carbon source. The response surface methodology model revealed the highest total nitrogen removal by WT14 occurred at 20.3 °C, 113.5 r·min-1, C/N 10.8, and pH 8.4. Under adapted environmental conditions, up to 55.9 mg·L-1·h-1 of ammonium nitrogen (NH4+-N) was removed by WT14, and its NH4+-N tolerance ability reached 2000 mg·L-1. In addition to the reported high NH4+-resistance of Alcaligenes faecalis, WT14 multiplied fast and had strong nitrate or nitrite removal capacity when high strength nitrate or nitrite was provided as the single nitrogen source; which differed from other Alcaligenes faecalis species. These results show WT14 is a novel strain of Alcaligenes faecalis and its nitrogen removal pathway will be carried out in the further study.

Nitrogen removal performance and needed area estimation of surface-flow constructed wetlands using a probabilistic approach.

Pollutant concentrations in influents into constructed wetlands (CWs) are highly fluctuating and may vary over several orders of magnitude, leading to large uncertainties in removal performance assessment when using pollutant concentrations in the influent and effluent directly. Incorporating a probabilistic approach into removal performance assessment and needed area estimation of CWs could advantage decision making regarding wastewater treatment and engineering applications. A series of three-stage surface-flow CWs (SFCWs) were constructed for treating ammonium-rich swine wastewater. The surface removal rate and removal efficiency of ammonium nitrogen in the SFCWs using the probabilistic approach were 0.27-3.23 g m-2 d-1 and 43.0-99.9% (95% confidence interval (CI)), which were consistent with the deterministic approach (95% CI: 0.24-3.18 g m-2 d-1 and 70.4-99.9%). The needed SFCW area was estimated as 6.6 (95% CI: 1.4-17.8) to 29.7 (95% CI: 6.4-80.1) m2 for required removal efficiency from 40% to 90% for 0.18 m3 d-1 swine wastewater with different strengthens. For specific removal efficiency of 90%, the needed CW areas was 13.9 (95%CI: 4.9-42.7), 25.1 (95%CI: 5.9-66.0), 33.5 (95%CI: 13.5-87.1), and 40.8 (95%CI: 16.2-89.4) m2 for influent ammonium loading rate of 0.18-2.7, 2.7-14.4, 14.4-36, and 36-60 g d-1, respectively. The first-order removal constant of ammonium nitrogen decreased logarithmically with increasing influent and effluent concentration/loading rate in the SFCW units (p < 0.001), which was responsible for the needed SFCW areas covering a wide range. The reliability analysis confirmed the results from the probabilistic approach were appropriate. The present study shed new lights on the performance evaluation and design of CWs for treating wastewater with highly-fluctuating concentrations using a probabilistic approach.

Correction to: Effects of long-term straw incorporation on lignin accumulation and its association with bacterial laccase-like genes in arable soils.

The first funding No. should be 41671298 instead of 41301298.

Effects of long-term straw incorporation on lignin accumulation and its association with bacterial laccase-like genes in arable soils.

In this study, we aimed to investigate lignin accumulation and its relationship with the composition of bacterial laccase-like genes in three arable lands (i.e., upland limestone soil (UL), upland red soil (UR), and upland-paddy rotation red soil (UPR)), which are subjected to long-term straw incorporation. After 9-13 years of straw incorporation, the lignin content significantly increased from 337.1, 414.5, and 201.6 mg/kg soil to 2096.5, 2092.4, and 1972.2 mg/kg soil in UL, UR, and UPR, respectively. The dominant lignin monomer changed from vanillyl (V)-type to cinnamyl (C)-type in UR. Both V- and C-types were the dominant monomers in UPR, and V-type monomer remained the dominant monomer in UL. Compared with the treatment without straw, straw incorporation significantly promoted the activity of laccase enzyme and the abundance of bacterial laccase-like genes in all soils. The redundancy analysis showed that the main influencing factors on lignin accumulation patterns with straw incorporation were the laccase enzyme activity, nitrogen availability, and some specific bacterial communities possessing the laccase-like genes (e.g., Thermotogae and Acidobacteria). The variation partitioning analysis confirmed that the strongest influencing factor on lignin accumulation was the composition of bacterial laccase-like genes (explained 31.4% of variance). The present study provides novel insights into the importance of bacterial laccase-like genes in shaping lignin monomer accumulation with straw incorporation in arable soils.

Robust and Accurate Hand-Eye Calibration Method Based on Schur Matric Decomposition.

To improve the accuracy and robustness of hand-eye calibration, a hand-eye calibration method based on Schur matric decomposition is proposed in this paper. The accuracy of these methods strongly depends on the quality of observation data. Therefore, preprocessing observation data is essential. As with traditional two-step hand-eye calibration methods, we first solve the rotation parameters and then the translation vector can be immediately determined. A general solution was obtained from one observation through Schur matric decomposition and then the degrees of freedom were decreased from three to two. Observation data preprocessing is one of the basic unresolved problems with hand-eye calibration methods. A discriminant equation to delete outliers was deduced based on Schur matric decomposition. Finally, the basic problem of observation data preprocessing was solved using outlier detection, which significantly improved robustness. The proposed method was validated by both simulations and experiments. The results show that the prediction error of rotation and translation was 0.06 arcmin and 1.01 mm respectively, and the proposed method performed much better in outlier detection. A minimal configuration for the unique solution was proven from a new perspective.

Enhanced nitrogen removal and quantitative analysis of removal mechanism in multistage surface flow constructed wetlands for the large-scale treatment of swine wastewater.

Constructed wetlands have recently been studied as a form of green infrastructure for the enhanced removal of nitrogen (N). This study aimed to demonstrate the use of multistage surface flow constructed wetland (SFCW) for treatment of swine wastewater. The results showed chemical oxygen demand (COD), total nitrogen (TN), NH4+, and NO3- removal rates of 16.3 g m-2 d-1, 9.14 g m-2 d-1, 7.75 g m-2 d-1, and 45.49 mg m-2 d-1, respectively. The sediment and plant absorption N rates were 2.44 g m-2 d-1, and 1.24 g m-2 d-1, respectively. Moreover, the microbial process which is the primary process, by which N is removed, accounted for 56.75-65.35%. Quantitative polymerase chain reaction (qPCR) revealed the highest microbial abundance in the segment of the SFCW with high N concentration. Ammonia-oxidizing bacteria (AOB) and nirK could be primarily responsible for the high removal rate of N. Factors like pH, DO, COD, N, and OM play an important role in influencing microbial abundance. It is suggested that the multistage SFCW has a promising future for the large scale treatment of swine wastewater.

Diversity and distribution of bacteria in a multistage surface flow constructed wetland to treat swine wastewater in sediments.

Managing waste produced from swine farming operations is a significant agricultural and environmental challenge. Confined animal feeding operations continually generate large amounts of animal waste, which necessitates adequate waste management systems. This study examines the use of multistage surface flow constructed wetlands (SFCWs) to treat pig farm sewage. The wastewater removal rate, sediment deposits, physicochemical properties, and microbial community compositions of each segment of a SFCW were examined. The results indicated that removal rates of chemical oxygen demand (COD), total nitrogen (TN), NH4+, NO3-, and total phosphorus (TP) were 89.8%, 97.9%, 98.2%, 87.6%, and 96.4%, respectively, in the multistage SFCW. The general trend showed increase in the dissolved oxygen (DO) concentrations and oxidation reduction potential (Eh) from the beginning of the SFCW to its end. Sediment concentrations of N and P in each segment of the SFCW generally decreased, suggesting their accumulation in each segment. High-throughput sequencing indicated that the bacterial diversity increased over time. Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were dominant in multistage SFCW bacterial communities at the phylum level. Results further indicate that DO and Eh are major environmental factors that influence the bacterial community distribution. Overall, our findings suggest that multistage SFCWs not only improve contaminant removal but also change the bacterial community composition and promote bacterial community diversity.

Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil.

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

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.