Positive soil priming effects are the rule at a global scale.

Priming effects of soil organic matter decomposition are critical to determine carbon budget and turnover in soil. Yet, the overall direction and intensity of soil priming remains under debate. A second-order meta-analysis was performed with 9296-paired observations from 363 primary studies to determine the intensity and general direction of priming effects depending on the compound type, nutrient availability, and ecosystem type. We found that fresh carbon inputs induced positive priming effects (+37%) in 97% of paired observations. Labile compounds induced larger priming effects (+73%) than complex organic compounds (+33%). Nutrients (e.g., N, P) added with organic compounds reduced the intensity of priming effects compared to compounds without N and P, reflecting "nutrient mining from soil organic matter" as one of the main mechanisms of priming effects. Notably, tundra, lakebeds, wetlands, and volcanic soils showed much larger priming effects (+125%) compared to soils under forests, croplands, and grasslands (+24…+32%). Our findings highlight that positive priming effects are predominant in most soils at a global scale. Optimizing strategies to incorporate fresh organic matter and nutrients is urgently needed to offset the priming-induced accelerated organic carbon turnover and possible losses.

Penguin-Driven Dissemination and High Enrichment of Antibiotic Resistance Genes in Lake Sediments across Antarctica.

Numerous penguins can propagate pathogens with antibiotic resistance genes (ARGs) into Antarctica. However, the effects of penguin dissemination on the lake ARGs still have received little attention via guano deposition. Here, we have profiled ARGs in ornithogenic sediments subject to penguin guano (OLS) and nonornithogenic sediments (NOLS) from 16 lakes across Antarctica. A total of 191 ARGs were detected in all sediment samples, with a much higher abundance and diversity in OLS than in NOLS. Surprisingly, highly diverse and abundant ARGs were found in the OLS with a detection frequency of >40% and an absolute abundance of (2.34 × 109)-(4.98 × 109) copies g-1, comparable to those in coastal estuarine sediments and pig farms. The strong correlations of identified resistance genes with penguin guano input amount, environmental factors, mobile genetic elements, and bacterial community, in conjunction with network and redundancy analyses, all indicated that penguins were responsible for the dissemination and high enrichment of ARGs in lake sediments via the guano deposition, which might greatly outweigh local human-activity effects. Our results revealed that ARGs could be carried into lakes across the Antarctica through penguin migration, food chains, and guano deposition, which were closely connected with the widespread pollution of ARGs at the global scale.

Antimicrobial peptides: An alternative to antibiotic for mitigating the risks of Antibiotic resistance in aquaculture.

The utilization of antibiotics increases the prevalence of antibiotic resistance genes (ARGs) in various matrices and poses the potential risk of ARG transmission, garnering global attention. Antimicrobial peptides (AMPs) represent a promising novel category of antimicrobials that may address the urgent issue of antibiotic resistance. Here, a zebrafish cultivation assay in which zebrafish were fed a diet supplemented with AMP (Cecropin A) or antibiotics was conducted to determine the effects of the intervention on the microorganisms and antibiotic resistance spectrum in zebrafish gut samples. Cecropin A treatment decreased the α-diversity of the microbiota. Moreover, NMDS (nonmetric multidimensional scaling) results revealed that the ß-diversity in the microbiota was more similar between the control (CK) and Cecropin A samples than between the antibiotic treatment groups. The absolute quantity of ARGs in the AMP treatment was less than that observed in the antibiotic treatment. The findings indicated that FFCH7168, Chitinibacter and Cetobacterium were the most significant biomarkers detected in the CK, Cecropin A and antibiotic treatments, respectively. Although the use of antibiotics notably enhanced the occurrence of multidrug-resistant bacteria, the application of Cecropin A did not lead to this phenomenon. The results indicated that the application of AMPs can effectively manage and control ARGs in aquaculture.

Hyperaccumulator extracts promoting the phytoremediation of rare earth elements (REEs) by Phytolacca americana: Role of active microbial community in rhizosphere hotspots.

The increased usage of rare earth elements (REEs) leads to the extensive exploitation of rare earth mines, and the REEs pollution in soil caused by the legacy mine tailings has brought great harm to environment and human health. Although Phytolacca americana can remove REEs from contaminated soil to some extent, there is still an urgent problem to improve its efficiency. Hyperaccumulator extract is a new organic material with potential in metal phytoextraction, but its role in REEs phytoremediation and the related underlying processes remain unclear. In this study, hyperaccumulator extracts from P. americana root (PR), stem (PS), leaf (PL) and EDTA were used to improve the phytoremediation efficiency of REEs with P. americana. Soil zymography was applied to assess the enzyme hotspots' spatial distribution in the rhizosphere, and the hotspots' microbial communities were also identified. The results indicated that the application of hyperaccumulator extracts improved the biomass and REEs uptake of P. americana, and the highest REEs content in plant was observed in the treatment of PS, which increased 299% compared to that of the control. Hotspots area of ß-glucosidase, leucine aminopeptidase and acid phosphatase were concentrated in the pant rhizosphere along the roots and increased 2.2, 5.3 and 2.2 times after PS application compared to unamended soils. The PS application increased the relative abundance of Proteobacteria, Cyanobacteria, Bacteroidota and Firmicutes phyla in rhizosphere. Soil fungi have a higher contribution on promoting REEs activation than that of bacteria. Available P and extractable REEs were leading predictors for the plant biomass and REEs concentrations. The co-occurrence network showed that the application of PS creates a more efficient and stable microbial network compared to other treatments. In conclusion, stem-derived hyperaccumulator extract is excellent in stimulating REEs phytoremediation with P. americana by improving hotspots microbial activities and form a healthy rhizosphere microenvironment.

The effect of the 13C abundance of soil microbial DNA on identifying labelled fractions after ultracentrifugation.

DNA-based stable isotope probing (DNA-SIP) technology has been widely employed to trace microbes assimilating target substrates. However, the fractions with labelled universal genes are sometimes difficult to distinguish when detected by quantitative real-time PCR. In this experiment, three paddy soils (AQ, CZ, and NB) were amended with 0.1% glucose containing 13C at six levels, and DNA was then extracted after a 7-day incubation and subjected to isopycnic gradient centrifugation. The results showed that the amount of labelled DNA was notably related to the 13C-glucose percentage, while the separation spans of 18S rRNA and 16S rRNA genes between labelled and unlabelled treatments became notably clearer when the δ13C values of the total DNA were 90.9, 61.6, and 38.9‰ and 256.2, 104.5 and 126.1‰ in the AQ, CZ, and NB soils, respectively. Moreover, fractionated DNA was also labelled by determining the δ13C values while adding only 5 atom% 13C-glucose to the soil. The results suggest that the optimal labelling fractions were not always those fractions with the maximal gene abundance, and detecting the δ13C values of the total and fractionated DNA was beneficial in estimating the results of DNA-SIP. KEY POINTS: • Appropriate 13C-DNA amount was needed for DNA-SIP. • Detecting the 13C ratio of fractionated DNA directly was an assistant method for identifying the labelled fractions. • Fractions with the maximal 18S or 16S rRNA gene abundance always were not labelled.

15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils.

Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3--N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different.

DNA-SIP delineates unique microbial communities in the rhizosphere of the hyperaccumulator Sedum alfredii which are beneficial to Cd phytoextraction.

Rhizo-microbe recruited by hyperaccumulating plants are crucial for the extraction of metals from contaminated soils. It is important, but difficult, to identify the specific rhizosphere microbes of hyperaccumulators shaped by root exudation. Continuous 13CO2 labeling, microbial DNA-based stable isotope probing (DNA-SIP), and high throughput sequencing were applied to identify those rhizosphere microorganisms using exudates from the Cd hyperaccumulator Sedum alfredii. In contrast to its non-hyperaccumulating ecotype (NAE), the hyperaccumulating ecotype (HAE) of S. alfredii strongly changed the rhizosphere environment and extracted a 5-fold higher concentration of Cd from contaminated soil. Although both HAE and NAE harbored Streptomyces, Massilia, Bacillus, and WPS-2 Uncultured Bacteria with relative abundance of more than 1% in the rhizosphere associated with plant growth and immunity, the HAE rhizosphere specifically recruited Rhodanobacter (2.66%), Nocardioides (1.16%), and Burkholderia (1.01%) through exudates to benefit the extraction of Cd from soil. Different from the bacterial network with weak cooperation in the NAE rhizosphere, a closed-loop bacterial network shaped by exudates was established in the HAE rhizosphere to synergistically resist Cd. This research reveals a specific rhizosphere bacterial community induced by exudates assisted in the extraction of Cd by S. alfredii and provides a new perspective for plant regulation of the rhizo-microbe community beneficial for optimizing phytoremediation.

Comparing the variations and influencing factors of CH4 emissions from paddies and wetlands under CO2 enrichment: A data synthesis in the last three decades.

Understanding and quantifying the impact of elevated tropospheric carbon dioxide concentration (e [CO2]) on methane (CH4) globally is important for effectively assessing and mitigating climate warming. Paddies and wetlands are the two important sources of CH4 emissions. Yet, a quantitative synthetic investigation of the effects of e [CO2] on CH4 emissions from paddies and wetlands on a global scale has not been conducted. Here, we conducted a meta-analysis of 488 observation cases from 40 studies to assess the long-term effects of e [CO2] (ambient [CO2]+ 53-400 µmol mol-1) on CH4 emissions and to identify the relevant key drivers. On aggregate, e [CO2] increased CH4 emissions by 25.7% (p < 0.05) from paddies but did not affect CH4 emissions from wetlands (-3.29%; p > 0.05). The e [CO2] effects on paddy CH4 emissions were positively related to that on belowground biomass and soil-dissolved CH4 content. However, these factors under e [CO2] resulted in no significant change in CH4 emissions in wetlands. Particularly, the e [CO2]-induced abundance of methanogens increased in paddies but decreased in wetlands. In addition, tillering number of rice and water table levels affected e [CO2]-induced CH4 emissions in paddies and wetlands, respectively. On a global scale, CH4 emissions changed from an increase (+0.13 and + 0.86 Pg CO2-eq yr-1) under short-term e [CO2] into a decrease and no changes (-0.22 and + 0.03 Pg CO2-eq yr-1) under long-term e [CO2] in paddies and wetlands, respectively. This suggested that e [CO2]-induced CH4 emissions from paddies and wetlands changed over time. Our results not only shed light on the different stimulative responses of CH4 emissions to e [CO2] from paddy and wetland ecosystems but also suggest that estimates of e [CO2]-induced CH4 emissions from global paddies and wetlands need to account for long-term changes in various regions.

Biofilm Formation and Control of Foodborne Pathogenic Bacteria.

Biofilms are microbial aggregation membranes that are formed when microorganisms attach to the surfaces of living or nonliving things. Importantly, biofilm properties provide microorganisms with protection against environmental pressures and enhance their resistance to antimicrobial agents, contributing to microbial persistence and toxicity. Thus, bacterial biofilm formation is part of the bacterial survival mechanism. However, if foodborne pathogens form biofilms, the risk of foodborne disease infections can be greatly exacerbated, which can cause major public health risks and lead to adverse economic consequences. Therefore, research on biofilms and their removal strategies are very important in the food industry. Food waste due to spoilage within the food industry remains a global challenge to environmental sustainability and the security of food supplies. This review describes bacterial biofilm formation, elaborates on the problem associated with biofilms in the food industry, enumerates several kinds of common foodborne pathogens in biofilms, summarizes the current strategies used to eliminate or control harmful bacterial biofilm formation, introduces the current and emerging control strategies, and emphasizes future development prospects with respect to bacterial biofilms.

Short-Term Benzalkonium Chloride (C12) Exposure Induced the Occurrence of Wide-Spectrum Antibiotic Resistance in Agricultural Soils.

Antibiotic resistance genes (ARGs) are global pollutants that pose a potential risk to human health. Benzalkonium chloride (C12) (BC) disinfectants are thought to exert selection pressure on antibiotic resistance. However, evidence of BC-induced changes in antibiotic resistance in the soil environment is lacking. Here, we established short-term soil microcosms to investigate ARG profile dynamics in agricultural soils amended with sulfamethazine (SMZ, 10 mg kg-1) and gradient concentrations of BC (0-100 mg kg-1), using high-throughput quantitative PCR and Illumina sequencing. With the increase in BC concentration, the number of ARGs detected in the soil increased, but the normalized ARG abundance decreased. The added SMZ had a limited impact on ARG profiles. Compared to broad-spectrum fungicidal BC, the specificity of SMZ significantly affected the microbial community. Network analysis found that low-medium BC exposure concentrations resulted in the formation of small but strong ARG co-occurrence clusters in the soil, while high BC exposure concentration led to a higher incidence of ARGs. Variation partitioning analysis suggested that BC stress was the major driver shaping the ARG profile. Overall, this study highlighted the emergence and spread of BC-induced ARGs, potentially leading to the antimicrobial resistance problem in agricultural soils.

Interactive effects of microplastics, biochar, and earthworms on CO2 and N2O emissions and microbial functional genes in vegetable-growing soil.

Soil carbon dioxide (CO2) and nitrous oxide (N2O) emissions are two main greenhouse gases that play important roles in global warming. Studies have shown that microplastics, biochar, and earthworms can significantly affect soil greenhouse gas emissions. However, few studies have explored how their interactions affect soil CO2 and N2O emissions. A mesocosm experiment was conducted to investigate their interactive effects on soil greenhouse gases and soil microbial functional genes in vegetable-growing soil under different incubation times. Biochar alone or combined with microplastics significantly decreased soil CO2 emissions but had no effect on soil N2O emissions. Microplastics and biochar inhibited CO2 emissions and promoted N2O emissions in the soil with earthworms. The addition of microplastics, biochar, and earthworms had significant effects on soil chemical properties, including dissolved organic carbon, ammonia nitrogen, nitrate nitrogen, total nitrogen, and pH. Microplastics and earthworms selectively influenced microbial abundances and led to a fungi-prevalent soil microbial community, while biochar led to a bacteria-prevalent microbial community. The interactions of microplastics, biochar, and earthworms could alleviate the reduction of the bacteria-to-fungi ratio and the abundance of microbial functional genes caused by microplastics and earthworms alone. Microplastics significantly inhibited microorganisms as well as C and N cycling functional genes in earthworm guts, while biochar obviously stimulated them. The influence of the addition of exogenous material on soil greenhouse gas emissions, soil chemical properties, and functional microbes differed markedly with soil incubation time. Our results indicated that biochar is a promising amendment for soil with microplastics or earthworms to simultaneously mitigate CO2 emissions and regulate soil microbial community composition and function. These findings contribute to a better understanding of the interaction effects of microplastics, biochar, and earthworms on soil carbon and nitrogen cycles, which could be used to help conduct sustainable environmental management of soil.

The enhanced degradation behavior of oxytetracycline by black soldier fly larvae with tetracycline resistance genes in the larval gut: Kinetic process and mechanism.

Black soldier fly larvae (larvae) can digest organic wastes and degrade contaminants such as oxytetracycline (OTC). However, compared to the kinetic processes and enhanced mechanisms used in the traditional microbial degradation of OTC, those employed by larvae are largely uncharacterized. To obtain further details, a combined analysis of larval development, larval nutritional values (crude protein, crude fat and the composition of fatty acids) and the expression of tetracycline resistance genes (TRGs) in the larval gut was performed for the degradation of OTC added to substrates and for oxytetracycline bacterial residue (OBR). When the larvae were exposed to the substrates, the degradation processes were enhanced significantly (P < 0.01), with a 4.74-7.86-fold decrease in the degradation half-life (day-1) and a 3.34-5.74-fold increase in the final degradation efficiencies. This result was attributed to the abundant TRGs (with a detection rate of 35.90%∼52.14%) in the larval gut. The TRGs presented the resistance mechanisms of cellular protection and efflux pumps, which ensured that the larvae could tolerate elevated OTC concentrations. Investigation of the TRGs indicated that enzymatic inactivation enhanced OTC degradation by larvae. These findings demonstrate that the larval degradation of antibiotic contaminants is an efficient method based on abundant TRGs in the larval gut, even though OTC degradation results in OBR. In addition, a more optimized system for higher reductions in antibiotic levels and the expansion of larval bioremediation to other fields is necessary.

Influence of reductive soil disinfestation or biochar amendment on bacterial communities and their utilization of plant-derived carbon in the rhizosphere of tomato.

Root-associated microorganisms play an important role in plant nutrition and productivity. However, our understanding of how a plant-microbiome system responds to pre-planting soil management remains limited. Here, continuous labeling with 13CO2 gas combined with stable isotope probing (SIP) was applied to explore bacterial utilization of plant-derived carbon (C) in the tomato rhizosphere as affected by biochar amendment or reductive soil disinfestation (RSD). Our results showed that RSD treatment strongly shaped the soil bacterial community composition, while biochar soil amendment had little impact on the community in the rhizosphere of tomato. We observed that the bacterial community in the RSD treatment, which actively utilized plant-derived C, belonged to various phyla (i.e., Proteobacteria, Cyanobacteria, Verrucomicrobia, and Acidobacteria), while the genus Streptomyces (phylum Actinobacteria) was the main bacterial taxa that actively utilized plant-derived C in the biochar and control treatments. This study provides evidence that biochar application or RSD pre-planting soil management practices induced distinct bacterial utilization of plant-derived C, which may in turn regulate plant productivity in agricultural systems. KEY POINTS: • Genus Streptomyces was the main bacterial group utilizing plant-derived carbon in both control and biochar treatments. • Reductive soil disinfestation altered bacterial utilization of plant-derived carbon. • Biochar did not alter the composition of the bacterial communities but had more labeled bacterial taxa utilizing plant-derived carbon.

Phosphorus Input Alters the Assembly of Rice (Oryza sativa L.) Root-Associated Communities.

Rice root-associated microbial community play an important role in plant nutrient acquisition, biomass production, and stress tolerance. Herein, root-associated community assembly was investigated under different phosphate input levels in phosphorus (P)-deficient paddy soil. Rice was grown in a long-term P-depleted paddy soil with 0 (P0), 50 (PL), or 200 (PH) mg P2O5 kg-1 application. DNA from root endophytes was isolated after 46 days, and PCR amplicons from archaea, bacteria, and fungi were sequenced by an Illumina Miseq PE300 platform, respectively. P application had no significant effect on rice root endophytic archaea, which were dominated by ammonia-oxidizing Candidatus Nitrososphaera. By contrast, rice root endophytic community structure of the bacteria and fungi was affected by soil P. Low P input increased endophytic bacterial diversity, whereas high P input increased rhizosphere fungi diversity. Bacillus and Pleosporales, associated with phosphate solubilization and P uptake, dominated in P0 and PH treatments, and Pseudomonas were more abundant in the PL treatment than in the P0 and PH treatments. Co-occurrence network analysis revealed a close interaction between endophytic bacteria and fungi. Soil P application affected both the rice root endosphere and soil rhizosphere microbial community and interaction between rice root endophytic bacteria, and fungi, especially species related to P cycling.

Limited effect of planting transgenic rice on the soil microbiome studied by continuous 13CO2 labeling combined with high-throughput sequencing.

The planting of transgenic rice has aroused ongoing controversy, due to the public anxiety surrounding the potential risk of transgenic rice to health and the environment. The soil microbial community plays an important environmental role in the plant-soil-microbe system; however, few studies have focused on the effect of transgenic rice on the soil rhizospheric microbiome. We labeled transgenic gene rice (TT51, transformed with Cry1Ab/1Ac gene), able to produce the Bt (Bacillus thuringiensis) toxin, its parental variety (Minghui 63), and a non-parental variety (9931) with 13CO2. The DNA of the associated soil rhizospheric microbes was extracted, subjected to density gradient centrifugation, followed by high-throughput sequencing of bacterial 16S rRNA gene. Unweighted unifrac analysis of the sequencing showed that transgenic rice did not significantly change the soil bacterial community structure compared with its parental variety. The order Opitutales, affiliated to phylum Verrucomicrobia and order Sphingobacteriales, was the main group of labeled bacteria in soil planted with the transgenic and parental varieties, while the orders Pedosphaerales, Chthoniobacteraceae, also affiliated to Verrucomicrobia, and the genus Geobacter, affiliated to class Deltaproteobacteria, dominated in the soil of the non-parental rice variety. The non-significant difference in soil bacterial community structure of labeled microbes between the transgenic and parental varieties, but the comparatively large difference with the non-parental variety, suggests a limited effect of planting transgenic Bt rice on the soil microbiome.

Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil.

Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH4 production and the abundances of mcrA genes and their transcripts, nitrate amendment showed inhibitory effects on them. The terminal restriction fragment length polymorphism (T-RFLP) analysis based on mcrA gene revealed that straw addition obviously changed methanogenic community structure. Based on mcrA gene level, straw-alone addition stimulated Methanosarcinaceaes at the early stage of incubation (first 11 days), but nitrate showed inhibitory effect. The relative abundance of Methanobacteriaceae was also stimulated by straw addition during the first 11 days. Furthermore, Methanosaetaceae were enriched by nitrate-alone addition after 11 days, while Methanocellaceae were enriched by nitrate addition especially within the first 5 days. The transcriptional methanogenic community indicated more dynamic and complicated responses to straw and/or nitrate addition. Based on mcrA transcript level, nitrate addition alone resulted in the increase of Methanocellaceae and the shift from Methanosarcinaceae to Methanosaetaceae during the first 5 days of incubation. Straw treatments increased the relative abundance of Methanobacteriaceae after 11 days. These results demonstrate that nitrate addition influences methanogens which are transcriptionally and functionally active and can alleviate CH4 production associated with straw amendment in paddy soil incubations, presumably through competition for common substrates between nitrate-utilizing organisms and methanogens.

Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil.

Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community.

Potential contribution of anammox to nitrogen loss from paddy soils in Southern China.

The anaerobic oxidation of ammonium (anammox) process has been observed in diverse terrestrial ecosystems, while the contribution of anammox to N2 production in paddy soils is not well documented. In this study, the anammox activity and the abundance and diversity of anammox bacteria were investigated to assess the anammox potential of 12 typical paddy soils collected in southern China. Anammox bacteria related to "Candidatus Brocadia" and "Candidatus Kuenenia" and two novel unidentified clusters were detected, with "Candidatus Brocadia" comprising 50% of the anammox population. The prevalence of the anammox was confirmed by the quantitative PCR results based on hydrazine synthase (hzsB) genes, which showed that the abundance ranged from 1.16 × 10(4) to 9.65 × 10(4) copies per gram of dry weight. The anammox rates measured by the isotope-pairing technique ranged from 0.27 to 5.25 nmol N per gram of soil per hour in these paddy soils, which contributed 0.6 to 15% to soil N2 production. It is estimated that a total loss of 2.50 × 10(6) Mg N per year is linked to anammox in the paddy fields in southern China, which implied that ca. 10% of the applied ammonia fertilizers is lost via the anammox process. Anammox activity was significantly correlated with the abundance of hzsB genes, soil nitrate concentration, and C/N ratio. Additionally, ammonia concentration and pH were found to be significantly correlated with the anammox bacterial structure.

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil.

The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array-based analysis revealed that long-term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer-induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P-limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions.

Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils.

Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.