The community composition of soil-denitrifying bacteria from a turfgrass environment

Diversity and abundance of denitrifiers during cow manure composting

Diversity and abundance of the denitrifying genes nirK, nirS and nosZ were investigated in cow manure compost using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time quantitative PCR (qPCR), respectively. These three genes were detected in all the stages of the composting process. Phylogenetic analysis showed that the nirK gene was closely related to Rhizobiales, Burkholderiales, the nirS gene was closely related to Pseudomonadales and Burkholderiales, and the nosZ gene was closely related to Rhodospirillales, Rhizobiales, Pseudomonadales, and Alteromonadales. qPCR results showed that the abundance of these three genes (nirK, nirS and nosZ) reached the peak value in the late thermophilic stage of composting and abundance of the nirK gene was higher than that of the nosZ gene and the nirS gene. Redundancy analysis (RDA) showed that the diversity of the nirK and nirS genes was significantly correlated with ammonium (p<0.05), the diversity of the nosZ gene was significantly correlated with pH (p<0.05) and the abundance of the nirK nirS and nosZ genes was significantly correlated with temperature (p<0.05).

The extent and pathways of nitrogen loss in turfgrass systems: Age impacts

Nitrogen loss from fertilized turf has been a concern for decades, with most research focused on inorganic (NO₃^-) leaching. The present work examined both inorganic and organic N species in leachate and soil N₂O emissions from intact soil cores of a bermudagrass chronosequence (1, 15, 20, and 109 years old) collected in both winter and summer. Measurements of soil N₂O emissions were made daily for 3 weeks, while leachate was sampled once a week. Four treatments were established to examine the impacts of fertilization and temperature: no N, low N at 30 kg N ha^-1, and high N at 60 kg N ha^-1, plus a combination of high N and temperature (13 °C in winter or 33 °C in summer compared to the standard 23 °C). Total reactive N loss generally showed a "cup" pattern of turf age, being lowest for the 20 years old. Averaged across all intact soil cores sampled in winter and summer, organic N leaching accounted for 51% of total reactive N loss, followed by inorganic N leaching at 41% and N₂O-N efflux at 8%. Proportional loss among the fractions varied with grass age, season, and temperature and fertilization treatments. While high temperature enhanced total reactive N loss, it had little influence on the partitioning of loss among dissolved organic N, inorganic N and N₂O-N when C availability was expected to be high in summer due to rhizodeposition and root turnover. This effect of temperature was perhaps due to higher microbial turnover in response to increased C availability in summer. However when C availability was low in winter, warming might mainly affect microbial growth efficiency and therefore partitioning of N. This work provides a new insight into the interactive controls of warming and substrate availability on dissolved organic N loss from turfgrass systems.

Microbial community characteristics during simultaneous nitrification-denitrification process: effect of COD/TP ratio

To evaluate the impact of chemical oxygen demand (COD)/total phosphorus (TP) ratio on microbial community characteristics during low-oxygen simultaneous nitrification and denitrification process, three anaerobic-aeration (low-oxygen) sequencing batch reactors, namely R1, R2, and R3, were performed under three different COD/TP ratios of 91.6, 40.8, and 27.6. The community structures of each reactor were analyzed via molecular biological technique. The results showed that the composition of ammonia-oxidizing bacteria (AOB) was affected, indicated by Shannon indexes of the samples from R1, R2, and R3. Nitrosomonas was identified to be the dominant AOB in all SBRs. Moreover, the copy numbers of nitrifiers were more than those of denitrifiers, and the phosphorus-accumulating organisms to glycogen-accumulating organisms ratio increased with the decrease of COD/TP ratio.

Acidophilic denitrifiers dominate the N2O production in a 100-year-old tea orchard soil

Aerobic denitrification is the main process for high N2O production in acid tea field soil. However, the biological mechanisms for the high emission are not fully understood. In this study, we examined N2O emission and denitrifier communities in 100-year-old tea soils with four pH levels (3.71, 5.11, 6.19, and 7.41) and four nitrate concentration (0, 50, 200, and 1000 mg kg(-1) of NO3 (-)-N) addition. Results showed the highest N2O emission (10.1 mg kg(-1) over 21 days) from the soil at pH 3.71 with 1000 mg kg(-1) NO3 (-) addition. The N2O reduction and denitrification enzyme activity in the acid soils (pH <7.0) were significantly higher than that of soils at pH 7.41. Moreover, TRF 78 of nirS and TRF 187 of nosZ dominated in soils of pH 3.71, suggesting an important role of acidophilic denitrifiers in N2O production and reduction. CCA analysis also showed a negative correlation between the dominant denitrifier ecotypes (nirS TRF 78, nosZ TRF 187) and soil pH. The representative sequences were identical to those of cultivated denitrifiers from acidic soils via phylogenetic tree analysis. Our results showed that the acidophilic denitrifier adaptation to the acid environment results in high N2O emission in this highly acidic tea soil.

Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils

Microorganisms are capable of producing N2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils.

Diversity and distribution of nirK-harboring denitrifying bacteria in the water column in the Yellow River estuary

We investigated the diversity and community composition of denitrifying bacteria in surface water from the Yellow River estuary. Our results indicated that the diversity of the denitrifying community in freshwater based on the nirK gene was higher than that in seawater. Furthermore, phylogenetic analysis suggested that the bacteria community could be distributed into eight clusters (Clusters I to VIII). Redundancy analysis (RDA) revealed that community compositions were related to multiple environment factors, such as salinity and nitrate concentration. The results of the present study have provided a novel insight into the denitrifying community in water columns in estuaries.

Genetic characterization of denitrifier communities with contrasting intrinsic functional traits

Microorganisms capable of denitrification are polyphyletic and exhibit distinct denitrification regulatory phenotypes (DRP), and thus, denitrification in soils could be controlled by community composition. In a companion study (Dörsch et al., 2012) and preceding work, ex situ denitrification assays of three organic soils demonstrated profoundly different functional traits including N(2) O/N(2) ratios. Here, we explored the composition of the underlying denitrifier communities by analyzing the abundance and structure of denitrification genes (nirK, nirS, and nosZ). The relative abundance of nosZ (vs. nirK + nirS) was similar for all communities, and hence, the low N(2) O reductase activity in one of the soils was not because of the lack of organisms with this gene. Similarity in community composition between the soils was generally low for nirK and nirS, but not for nosZ. The community with the most robust denitrification (consistently low N(2) O/N(2) ) had the highest diversity/richness of nosZ and nirK, but not of nirS. Contrary results found for a second soil agreed with impaired denitrification (low overall denitrification activity, high N(2) O/N(2) ). In conclusion, differences in community composition and in the absolute abundance of denitrification genes clearly reflected the functional differences observed in laboratory studies and may shed light on differences in in situ N(2) O emission of the soils.

Effect of pyrene on denitrification activity and abundance and composition of denitrifying community in an agricultural soil

Toxicity of pyrene on the denitrifiers was studied by spiking an agricultural soil with pyrene to a series of concentrations (0-500 mg kg(-1)) followed by dose-response and dynamic incubation experiments. Results showed a positive correlation between potential denitrification activity and copy numbers of denitrifying functional genes (nirK, nirS and nosZ), and were both negatively correlated with pyrene concentrations. Based on the comparison of EC(50) values, denitrifiers harboring nirK, nirS or nosZ gene were more sensitive than denitrification activity, and denitrifiers harboring nirS gene were more sensitive than that harboring nirK or nosZ genes. Seven days after spiking with EC(50) concentration of pyrene, denitrifiers diversity decreased and community composition changed in comparison with the control. Phylogenetic analyses of three genes showed that the addition of pyrene increased the proportion of Bradyrhizobiaceae, Rhodospirillales, Burkholderiales and Pseudomonadales. Some species belonging to these groups were reported to be able to degrade PAHs.