Straw decreased N2O emissions from flooded paddy soils via altering denitrifying bacterial community compositions and soil organic carbon fractions

Straw return is widely applied to increase soil fertility and soil organic carbon storage. However, its effect on N2O emissions from paddy soil and the associated microbial mechanisms are still unclear. In this study, wheat straw was amended to two paddy soils (2% w/w) from Taizhou (TZ) and Yixing (YX), China, which were flooded and incubated for 30 d. Real-time PCR and Illumina sequencing were used to characterize changes in denitrifying functional gene abundance and denitrifying bacterial communities. Compared to unamended controls, straw addition significantly decreased accumulated N2O emissions in both TZ (5071 to 96 mg kg-1) and YX (1501 to 112 mg kg-1). This was mainly due to reduced N2O production with decreased abundance of major genera of nirK and nirS-bacterial communities and reduced nirK and nirS gene abundances. Further analyses showed that nirK-, nirS- and nosZ-bacterial community composition shifted mainly along the easily oxidizable carbon (EOC) arrows following straw amendment among four different soil organic carbon fractions, suggesting that increased EOC was the main driver of alerted denitrifying bacterial community composition. This study revealed straw return suppressed N2O emission via altering denitrifying bacterial community compositions and highlighted the importance of EOC in controlling denitrifying bacterial communities.

Coupling between Nitrification and Denitrification as well as Its Effect on Phosphorus Release in Sediments of Chinese Shallow Lakes

The coupling of nitrification and denitrification has attracted wide attention since it plays an important role in mitigating eutrophication in aquatic ecosystems. However, the underlying mechanism is largely unknown. In order to study the coupling relationship between nitrification and denitrification, as well as its effect on phosphorus release, nutrient levels, functional gene abundance and potential rates involved in nitrification and denitrification were analyzed in three shallow urban lakes with different nutrient status. Trophic level was found positively related to not only copy numbers of functional genes of nitrosomonas and denitrifiers, but also the potential nitrification and denitrification rates. In addition, the concentrations of different forms of phosphorus showed a positive correlation with the number of nitrosomonas and denitrifiers, as well as potential nitrification and denitrification rates. Furthermore, the number of functional genes of nitrosomonas exhibited positive linear correlations with functional genes and rate of denitrification. These facts suggested that an increase in phosphorus concentration might have promoted the coupling of nitrification and denitrification by increasing their functional genes. Strong nitrification–denitrification fueled the nitrogen removal from the system, and accelerated the phosphorus release due to the anaerobic state caused by organic matter decomposition and nitrification. Moreover, dissolved organic nitrogen was also released into the water column during this process, which was favorable for balancing the nitrogen and phosphorus ratio. In conclusion, the close coupling between nitrification and denitrification mediated by nitrifier denitrification had an important effect on the cycling mode of nitrogen and phosphorus.

Cause and effect of N/P ratio decline with eutrophication aggravation in shallow lakes

To explore the relationship and cause and effect between eutrophication and the nitrogen (N)/phosphorus (P) ratio, samples from 38 lakes in Wuhan City, China, with differing degrees of eutrophication, were collected for nutrient levels and extracellular enzyme activities (EEA) in the water column from July 2011 to November 2011. The phosphorus fraction, abundance and potential denitrification rate (PDR) as well as community composition of nirS-type denitrifier in sediments of five typical lakes were further analyzed. A higher trophic level index (TSI) corresponded to a lower N/P ratio, which can be attributed to a loss of N and an increase in P. Specifically, in more eutrophic lakes, the enrichment of total organic carbon and all forms of P in sediments could fuel PDR by shaping community composition and increasing the abundance of nirS-type denitrifier as evidenced by correlation and redundancy analysis, ultimately resulting in a loss of N. Meanwhile, iron-bound phosphorus release induced by anoxia and the hydrolysis of organic P accounted for the observed increase of P in the water column. The lower N/P ratio facilitated the production of leucine aminopeptidase, which was unexpectedly induced by high P but not by low N. Similarly, alkaline phosphatase was induced by high N but not by low P. These findings indicate a mutual coupling and interplay between N and P cycling and confirm our hypothesis that P accumulation accelerates N loss in the process of eutrophication.

Urea Amendment Decreases Microbial Diversity and Selects for Specific Nitrifying Strains in Eight Contrasting Agricultural Soils

Application of nitrogen (N) fertilizers, predominantly as urea, is a major source of reactive N in the environment, with wide ranging effects including increased greenhouse gas accumulation in the atmosphere and aquatic eutrophication. The soil microbial community is the principal driver of soil N cycling; thus, improved understanding of microbial community responses to urea addition has widespread implications. We used next-generation amplicon sequencing of the 16S rRNA gene to characterize bacterial and archaeal communities in eight contrasting agricultural soil types amended with 0, 100, or 500 μg N g^-1 of urea and incubated for 21 days. We hypothesized that urea amendment would have common, direct effects on the abundance and diversity of members of the microbial community associated with nitrification, across all soils, and would further affect the broader heterotrophic community resulting in decreased diversity and variation in abundances of specific taxa. Significant (P < 0.001) differences in bacterial community diversity and composition were observed by site, but amendment with only the greatest urea concentration significantly decreased Shannon indices. Expansion in the abundances of members of the families Microbacteriaceae, Chitinophagaceae, Comamonadaceae, Xanthomonadaceae, and Nitrosomonadaceae were also consistently observed among all soils (linear discriminant analysis score ≥ 3.0). Analysis of nitrifier genera revealed diverse, soil-specific distributions of oligotypes (strains), but few were correlated with nitrification gene abundances that were reported in a previous study. Our results suggest that the majority of the bacterial and archaeal community are likely unassociated with N cycling, but are significantly negatively impacted by urea application. Furthermore, these results reveal that amendment with high concentrations of urea may reduce nitrifier diversity, favoring specific strains, specifically those within the nitrifying genera Nitrobacter, Nitrospira, and Nitrosospira, that may play significant roles related to N cycling in soils receiving intensive urea inputs.

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China

Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.

Biochar decreases nitrogen oxide and enhances methane emissions via altering microbial community composition of anaerobic paddy soil

Biochar application to agricultural soil is an appealing approach to mitigate nitrous oxide (N₂O) and methane (CH₄) emissions. However, the underlying microbial mechanisms are unclear. In this study, a paddy soil slurry was incubated anaerobically for 14d with biochar amendments produced from rice straw at 300, 500, or 700°C (B300, B500, and B700) to study their influences on greenhouse gas emissions. Illumina sequencing was used to characterize shift of soil bacterial and archaeal community composition. After peaking at day 1, N₂O emission then sharply decreased to low levels while CH₄ started to emit at day 3 then continually increased with incubation. Compared to control soil (57.9mgkg^-1 soil), B300, B500, and B700 amendments decreased N₂O peak emission to 17.9, 1.28, and 0.59mgkg^-1, mainly due to increased soil pH. In contrast, the amendments enhanced CH₄ production from 58.2 to 93.4, 62.6, and 63.4mgkg^-1 at day 14 due to increased soil dissolved organic carbon. Abundance of denitrifying bacteria (e.g., Bacilli, 7.07-13.6 vs. 16.9%) was reduced with biochar amendments, especially with B500 and B700, contributing to the decreased N₂O emissions. However, larger pore size of B500 and B700 (surface area of 68.1 and 161m²g^-1) than B300 (4.40m²g^-1) favored electron transfer between bacteria and iron minerals, leading to increased abundance of iron-reducing bacteria, (e.g., Clostridia, 48.2-50.6 vs. 33.3%), which competed with methanogens to produce CH₄, thereby leading to lower increase in CH₄ emission. Biochar amendments with high pH and surface area might be effective to mitigate emission of both N₂O and CH₄ from paddy soil.

Temporal Variations in Diazotrophic Communities and nifH Transcripts Level Across the Agricultural and Fallow Land at Jaipur, Rajasthan, India

Biological nitrogen fixation is one of the most important nutrient processes in the ecosystem. Many studies have estimated the variations in soil diazotrophic communities across the globe. To understand the dynamics of nitrogen fixing bacterial communities and their response to the environmental changes, it is important to study the temporal variability of these communities. Using DNA fingerprinting method, denaturing gradient gel electrophoresis and real time polymerase chain reaction of the nifH gene, we have found that the agricultural land harbored unique nitrogen fixing communities that revealed different temporal patterns and abundance. Variation in soil moisture, organic carbon content, ammonium and nitrate concentrations may be the main factors which influenced the diazotrophic community composition and nifH gene abundance. Azospirillum species were more dominant in the agricultural soil. Unique environmental factors and agricultural practices were responsible for the temporal shifts in bacterial community structures and nifH transcripts level. Our study expands understanding of the influence of environmental factors on diazotrophic population that contributes to the nitrogen pool.

Microbial diversity of extreme habitats in human homes

High-throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions. These same environmental extremes can also be found closer to humans, even in our homes. Here, we used high-throughput sequencing techniques to assess bacterial and archaeal diversity in the extreme environments inside human homes (e.g., dishwashers, hot water heaters, washing machine bleach reservoirs, etc.). We focused on habitats in the home with extreme temperature, pH, and chemical environmental conditions. We found a lower diversity of microbes in these extreme home environments compared to less extreme habitats in the home. However, we were nonetheless able to detect sequences from a relatively diverse array of bacteria and archaea. Habitats with extreme temperatures alone appeared to be able to support a greater diversity of microbes than habitats with extreme pH or extreme chemical environments alone. Microbial diversity was lowest when habitats had both extreme temperature and one of these other extremes. In habitats with both extreme temperatures and extreme pH, taxa with known associations with extreme conditions dominated. Our findings highlight the importance of examining interactive effects of multiple environmental extremes on microbial communities. Inasmuch as taxa from extreme environments can be both beneficial and harmful to humans, our findings also suggest future work to understand both the threats and opportunities posed by the life in these habitats.

Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity

Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic–inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen–fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha diversity.