渭北旱塬长期施肥试验中氨氧化细菌的多样性及群落结构分析

以中国科学院长武黄土高原农业生态试验站23 a长期施肥定位试验的土壤样品为研究对象,通过构建氨氧化细菌的amoA基因克隆文库,采用PCR-RFLP方法分析了裸地（LD）、种植不施肥（CK）、单施氮肥（N）、单施磷肥（P）和氮磷共施（NP）这5个处理条件下土壤中氨氧化细菌的多样性及其群落结构。结果表明,N处理的土壤中氨氧化细菌的Shannon-Wiene（rH′）和Margalef（dM）a指数均最高,其次是CK、NP、P,而LD处理中最低,表明长期单施氮肥后增加了土壤中氨氧化细菌的多样性和丰富度,长期种植作物后也同样会增加土壤中氨氧化细菌的多样性和丰富度,但单施磷肥和氮磷共施后土壤中氨氧化细菌的多样性和丰富度都有所降低。基于amoA基因建立的系统进化树显示,所有来自于各处理条件下土壤中氨氧化细菌的优势种群都是属于Nitrosospira和Nitrosospira-like,与Nitrosospira cluster 3聚为一组,但优势菌种在克隆文库中所占的比例不同,表明不同的施肥处理下土壤中氨氧化细菌的群落结构发生了改变。     

Archaeal populations in biological soil crusts from arid lands in North America

Archaea are common and abundant members of biological soil crust communities across large-scale biogeographic provinces of arid North America. Regardless of microbial community development, archaeal populations averaged 2 × 10⁷ 16S rRNA gene copies per gram of soil, representing around 5% of the prokaryotic (total calculated bacterial and archaeal) numbers assessed by quantitative-PCR. In contrast, archaeal diversity, determined by denaturing gradient gel electrophoresis fingerprinting and clone libraries of 16S rRNA genes, was very restricted. Only six different phylotypes (all Crenarchaea) were detected, three of which were very dominant. Some phylotypes were widespread, while others were typical of Southern desert areas.     

Diversity of 16S-rRNA and nifH genes derived from rhizosphere soil and roots of an endemic drought tolerant grass,Lasiurus sindicus

Lasiurus sindicus is a highly nutritive, drought tolerant, perennial grass, endemic to the Thar Desert of Rajasthan, India. In order to characterize the diversity of bacteria associated with roots of this grass that had survived severe drought stress, 16S-rRNA gene clone libraries were established from RT-PCR amplified products of the total RNA extracted from the washed roots and rhizosphere soil samples. Eight major bacterial taxa were identified in a total of 121 16S-rRNA gene clones. The majority of sequences belonged to Gram-positive bacteria, Actinobacteria being the most predominant ones, closely followed by Firmicutes. Most of the sequences showed similarity with sequences from cultivated bacteria or uncultivated environmental clones associated with arid, semi-arid environments, cold deserts and contaminated soils. PCR amplification of nifH genes using total DNA as template produced a total of 48 nifH clones from the rhizosphere soil and root samples and revealed a predominance of nifH sequences closely affiliated to Pseudomonas pseudoalcaligenes, isolated in a previous study from root samples of Lasiurus sindicus. Some nifH sequences showed close similarity to cultivated diazotrophs like Azospirillum brasilense, Rhizobium sp., and a variety of uncultured nitrogen fixing bacteria. Thus, this study provides us with evidence that L. sindicus harbors a diversity of bacteria with potential for nitrogen fixation.     

The effects of combinations of biochar,lime, and organic fertilizer on nitrification and nitrifiers

Here, we report results from a field experiment investigating the application of biochars, lime, organic fertilizer, and their combinations. Soil pH was increased by ameliorants. Wheat biochar produced the largest increase, of approximately 2 pH units, and mixed treatment (one third rice husk biochar, one third lime, and one third organic fertilizer) also caused large increases, of almost 1 pH unit. There was strong evidence that the ratio of ammonia-oxidizing archaea to ammonia-oxidizing bacteria (AOB) abundance greatly increased with decreased soil pH, indicating that soil pH was an important factor affecting the abundance of AOB. High-throughput MiSeq sequencing showed that the soil ameliorants significantly increased the relative abundances of Nitrosomonas and Nitrospira. Soil pH was an important determinant of the bacterial community composition and diversity. Our study suggests that the ameliorants (biochar, lime, organic fertilizer, and their combinations) change soil nitrification by altering nitrifying bacteria abundance, diversity, and composition, caused by the changed soil pH.     

Amendment of degraded desert soil with wastewater debris containing immobilized Chlorella sorokiniana and Azospirillum brasilense significantly modifies soil bacterial community structure, diversity, and richness

The main goal of this study was to expand our knowledge of what happens to the soil bacterial community in an eroded desert soil when improvement of soil fertility is derived from the application of debris of tertiary wastewater treatment containing immobilized microalgae Chlorella sorokiniana and the plant growth-promoting bacterium (PGPB) Azospirillum brasilense. We hypothesized that an “improved” non-agricultural desert soil will exhibit substantial changes in the structure of the bacterial community in a relatively short time after amendment. To assess the effect of the amendments, microalgae and PGPB alone or combined, on the structure of the rhizosphere bacterial community, changes in species richness and bacterial diversity over time were based on sequence differences in the 16S rRNA gene, performed with PCR–denaturing gradient gel electrophoresis (DGGE) and then analyzed by similarity test and non-metric multidimensional scaling analysis. Root surface colonization and persistence in the rhizosphere of A. brasilense was monitored by fluorescent in situ hybridization and sequencing of DGGE bands. Application of waste debris significantly changed the rhizosphere bacterial population structure, whether comparisons were made over time, between inoculated and non-inoculated soil, and among different inoculated microorganisms. Species richness and diversity increased when the waste debris contained the microalgae–bacteria association and also over time. Even as its secondary role as an inoculant after wastewater treatment, A. brasilense colonized the root surface profusely and persisted within the rhizosphere bacterial community. This study demonstrated that small organic amendment to desert soil significantly changed soil bacterial community compared to the original soil and also 2 months after amendments were added.     

Does microbial habitat or community structure drive the functional stability of microbes to stresses following re-vegetation of a severely degraded soil?

Re-vegetation of eroded soil restores organic carbon concentrations and improves the physical stability of the soil, which may then extend the range of microhabitats and influence soil microbial activity and functional stability through its effects on soil bacterial community structure. The objectives of this study were (i) to evaluate the restorative effect of re-vegetation on soil physical stability, microbial activity and bacterial community structure; (ii) to examine the effects of soil physical microhabitats on bacterial community structure and diversity and on soil microbial functional stability. Soil samples were collected from an 18-year-old eroded bare soil restored with either Cinnamomum camphora (“Eroded Cc”) or Lespedeza bicolour (“Eroded Lb”). An uneroded soil planted with Pinus massoniana (“Uneroded Pm”) and an eroded bare soil served as references. The effect of microhabitats was assessed by physical destruction with a wet shaking treatment. Soil bacterial community structure and diversity were measured using a terminal restriction fragment length polymorphism (T-RFLP) approach, while soil microbiological stability (resistance and resilience) was determined by measuring short-term (28 days) decomposition rate of added barley (Hordeum vulgare) powder following copper and heat perturbations. The results demonstrated that re-vegetation treatment affected the recovery of physical and biological stability, microbial decomposition and the bacterial community structure. Although the restored soils overshot the Uneroded Pm sample in physical stability, they had lower microbial decomposition and less resilience to copper and heat perturbations than the Uneroded Pm samples. Soil physical destruction by shaking had the same effect on soil physical stability, but different effects on soil microbial functional stability. There were significant effects of vegetation treatment and perturbation type, and interactive effects among vegetation treatment, shaking and perturbation type on bacterial community structure. The destruction of aggregate structure increased resilience of the Eroded Lb sample and also altered its bacterial community structure. Both copper and heat perturbations resulted in significantly different community structure from the unperturbed controls, with a larger effect of copper than heat perturbation. Bacterial diversity (Shannon index) increased following the perturbations, with a more profound effect in the Uneroded Pm sample than in the restored soils. The interactive effects of vegetation treatment and shaking on microbial community and stability suggest that soil aggregation may contribute to the generation of bacterial community structure and mediation of biological stability via the protection afforded by soil organic carbon. Differential effects of re-vegetation treatment suggest that the long-term effects are mediated through changes in the quality and quantity of C inputs to soil.     

Balanced fertilization improved soil ammonia-oxidizing bacterial community in latosolic red soil

Abstract

We investigated the impact of nitrogen (N), phosphorus (P), potassium (K) (NPK) and NPK plus glucose-balanced fertilization compared with N-only fertilization on the soil pH, NH₄ ⁺, NO₃ ^?, ammonia-oxidizing bacterial community, bacterial community and function during microcosm incubation. The NPK and NPK plus glucose treatments resulted in significantly reducing soil acidification and NO₃ ^? accumulation compared with the N-only fertilization. The terminal restriction fragment size measuring 283 (Nitrosospira) and 54 bp (unidentified) were predominant in the soil ammonia-oxidizing bacterial composition for all treatments. The N-only fertilization did not change the ammonia-oxidizing bacterial community, the bacterial community composition based on terminal restriction fragment length polymorphism analysis, and the bacterial functional diversity based on Biolog EcoPlate^TM incubation. The NPK and NPK plus glucose treatments resulted in a shift in the soil ammonia-oxidizing bacterial community and bacterial community composition, and significantly increased the bacterial functional diversity (average well colour development, Richness and Shannon index). Nitrosomonas species were detected in the soil upon NPK and NPK plus glucose treatment on incubation day 9 but not on days 1 and 31. The effect of NPK treatment on the bacterial community composition was transient; a new 116 bp fragment was present on incubation day 9, but the data returned to their original values by day 31. In contrast, treatment with NPK plus glucose resulted in the appearance of a new 116 bp fragment that remained until incubation day 31. These results demonstrated that the balanced fertilization of N, P, K and glucose, plays an important role in regulating ammonia-oxidizing bacterial community quickly, and promoting nitrification functions. The results also showed the importance of balanced fertilization in reducing acidification, improving bacterial community structure and function in latosolic red soil. Therefore, optimizing the ammonia oxidation process by balanced fertilization may be helpful to reduce the loss of soil nitrogen.     

Microarray analysis of bacterial diversity and distribution in aggregates from a desert agricultural soil

Previous research has shown that soil structure can influence the distribution of bacteria in aggregates and, thereby, influence microbiological processes and diversity at small spatial scales. Here, we studied the microbial community structure of inner and outer fractions of microaggregates of a desert agricultural soil from the Imperial Valley of Southern California. To study the distribution of soil bacteria, 1,536 clones were identified using phylogenetic taxon probes to classify arrays of 16S rRNA genes. Among the predominant taxonomic groups were the α-Proteobacteria, Planctomycetes, and Acidobacteria. When compared across all phyla, the taxonomic compositions and distributions of bacterial taxa associated with the inner and outer fractions were nearly identical. Our results suggest that the ephemeral nature of soil aggregates in desert agricultural soils may reduce differences in the spatial distribution of bacterial populations as compared to that which occur in soils with more stable aggregates.     

Two- and three-domain bacterial laccase-like genes are present in drained peat soils

Laccases of fungal origin have been intensively studied due to their importance in various biotechnological applications. There is a constant demand for new laccases with improved properties such as stability at higher temperatures or at an alkaline pH. Growing molecular evidence suggests that laccases may also be widespread in bacteria. While only a handful of bacterial laccases have been purified and characterized, several novel traits have already been discovered (e.g. pH-stability and 2-domain organization of the enzyme as opposed to the usual 3-domain structure of fungal laccases). The aim of this study was to examine the diversity of bacterial laccase-like genes in two types of high-organic peat soil using a cloning and sequencing approach. Gene libraries prepared of small fragments (150 base pairs) revealed an amazing diversity of bacterial laccases. The fragments clustered in 11 major lineages, and one third of the 241 sequences resembled laccase-like genes of Acidobacteria. Additionally, a new primer was used to retrieve several larger fragments of the putative bacterial laccase genes that spanned all four copper-binding sites. Both “conventional” 3-domain laccases and the recently described 2-domain small laccases have been obtained using this approach, demonstrating the potential of the primer. The present study thus contributes to the understanding of the diversity of bacterial laccases and provides a new tool for finding laccase-like sequences in bacterial strains and soil samples.     

Anammox bacterial abundance and biodiversity in greenhouse vegetable soil are influenced by high nitrate content

The anaerobic ammonium oxidizing(anammox) process has been found to play an important role in terrestrial ecosystems in recent years. However,the diversity and abundance of anammox bacteria in nitrogen(N)-rich agricultural soils under high fertilizer greenhouse conditions are still unclear. Two greenhouse fields with different N fertilizer input levels were chosen, and their soil profiles were studied with molecular technologies, including quantitative polymerase chain reaction assay, a clone library, and phylogenetic analysis based on hzsB(encoding anammox hydrazine synthase β-subunit) gene. Molecular analyses suggested that anammox bacteria were at their highest density at 10–20 cm soil depth, and that the anammox bacterial abundance was significantly lower at high N than at low N. Candidatus Brocadia was the sole anammox bacterial genus throughout the soil depth profiles. The highest diversity of anammox bacteria was found at 30–40 cm soil depth, and different phylotypic clusters of Candidatus Brocadia were associated with specific soil environmental factors, such as nitrates, soil depth, and total N. Correlation analyses and redundancy analyses confirmed that high nitrate content associated with high N fertilizer input had a significant negative influence on the abundance and biodiversity of anammox bacteria. These results imply that excessive use of N fertilizer would affect arid land soil N loss to the atmosphere by the anammox pathway.     

Community composition of ammonia-oxidizing bacteria in the rhizosphere of intercropped wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.), maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.), and faba bean (<Emphasis Type="Italic">Vicia faba</Emphasis> L.)

Cereal/cereal and cereal/legume intercropping systems are popular in the north, northwest, and southwest of China and often result in yield increases compared to monocropping. Rhizosphere interactions may play a significant role in the yield increases, particularly with respect to nutrient availability. The aim of this study was to investigate the effects of intercropping on N availability and community composition of ammonia-oxidizing bacteria in the rhizosphere of wheat, maize, and faba bean at different growth stages. Denaturing gradient gel electrophoresis (DGGE) based on 16S rRNA genes was used to analyze the community composition of bacterial ammonia oxidizers belonging to β-proteobacteria. The results showed that intercropping with faba bean significantly increased nitrate concentrations in the rhizosphere of wheat and maize at the second sampling time (20 June) compared to monocropping or intercropping between maize and wheat. Intercropping significantly affected the community composition of ammonia-oxidizing bacteria in the rhizosphere compared to monocropping, and the effects were most pronounced in the maize/faba bean and wheat/maize intercropping systems when faba bean and wheat were at anthesis and maize was in seedling stage. In wheat/faba bean intercropping, the effects of intercropping on community composition of ammonia-oxidizing bacteria were less pronounced at the seedling stage of the two species but were significant at anthesis.     

Influence of bacterial-feeding nematodes on nitrification and the ammonia-oxidizing bacteria (AOB) community composition

The effects of bacterial-feeding nematodes on nitrification and the ammonia-oxidizing bacteria (AOB) community composition were studied in soil microcosms. Sterilized soils were inoculated with mixed soil bacteria (obtained by filtering) or with bacteria and bacterial-feeding nematodes, after which the dynamic inorganic nitrogen concentration was measured weekly. After 28 days of incubation, denaturing gradient gel electrophoresis (DGGE) based on PCR amplification of the amoA gene was used to analyze the AOB community composition. In addition, a clone library from the amoA gene fragments was established using clones randomly selected and sequenced from the two treatments. The results showed that the presence of bacterial-feeding nematodes led to significantly greater NH₄⁺ and NO₃⁻ contents over the entire incubation period, indicating that bacterial-feeding nematodes promoted both N mineralization and nitrification. The results of DGGE showed that the AOB community composition was significantly changed in the presence of bacterial-feeding nematodes. Furthermore, the sequencing results suggested that Nitrosospira sp. was the dominant species in the treatment without nematodes, while Nitrosomonas sp. and Nitrosospira sp. were the dominant species in the treatment with nematodes. Such changes in the AOB community may be one of explanation of the important role that nematodes play in promoting nitrification.     

Abundance and diversity of sulphur-oxidising bacteria and their role in oxidising elemental sulphur in cropping soils

There is an increasing interest in elemental S as a S fertiliser source, but to be available to plants, elemental S has to be oxidised to sulphate. Elemental S oxidation is known to be affected by soil properties and environmental conditions, but it is still unclear if elemental S oxidation is related to the abundance and diversity of S-oxidising bacteria in cropping soils. In this study, we investigated the abundance and diversity of S-oxidising bacteria by targeting a functional gene (soxB) and assessed their relationship with elemental S oxidation in ten cropping soils. Positive correlations between soil C, N and S contents on the one hand and the abundances of soxB and 16S ribosomal deoxyribonucleic acid (rRNA) genes on the other suggested that the abundances of S oxidising bacteria in particular and of bacteria in general depend on soil C and nutrient supply. Both soxB and 16S rRNA gene abundances were significantly correlated with the oxidation rate of elemental S (P < 0.05). In addition, more than 80% of the variation in the oxidation rate of elemental S could be explained by the combination of soxB or 16S rRNA gene abundances and soil pH, suggesting that pH not only affected bacterial abundances but also their activity during elemental S oxidation. Clone libraries constructed with the soxB primers showed genera belonging to Alphaproteobacteria, Betaproteobacteria and Deltaproteobacteria and Actinobacteria. The phylogenetic diversity and relative distribution of soxB clones revealed great differences across soils. However, no direct linkage was found between the diversity of S-oxidising bacteria and elemental S oxidation rate.     

两种农田土壤中的氨氧化细菌和氨氧化古菌对硝化抑制剂DCD和DMPP的响应-盆栽试验

Taking two important agricultural soils with different pH, brown soil （Hap-Udic Luvisol） and cinnamon soil （Hap-Ustic Luvisol）, from Northeast China, a pot culture experiment with spring maize （Zea mays L.） was conducted to study the dynamic changes in the abundance and diversity of soil ammonia-oxidizing bacteria （AOB） and ammonia-oxidizing archaea （AOA） populations during maize growth period in response to the additions of nitrification inhibitors dicyandiamide （DCD） and 3,4-dimethylpyrazole phosphate （DMPP） by the methods of real-time polymerase chain reaction （PCR） assay, PCR-denaturing gradient gel electrophoresis （DGGE）, and construction of clone library targeting the amoA gene. Four treatments were established, i.e., no urea （control）, urea, urea plus DCD, and urea plus DMPP. Both DCD and DMPP inhibited growth of AOB significantly, compared to applying urea alone. Soil bacterial amoA gene copies had a significant positive linear correlation with soil nitrate content, but soil archaeal amoA gene copies did not. In both soils, all AOB sequences fell within Nitrosospira or Nitrosospira-like groups, and all AOA sequences belonged to group 1.1b crenaxchaea. With the application of DCD or DMPP, community composition of AOB and AOA in the two soils had less change except that the AOB community composition in Hap-Udic Luvisol changed at the last two growth stages of maize under the application of DCD. AOB rather than AOA likely dominated soil ammonia oxidation in these two agricultural soils.     

Leaf litter is the main driver for changes in bacterial community structures in the rhizosphere of ash and beech

The rhizosphere and the surrounding soil harbor an enormous microbial diversity and a specific community structure, generated by the interaction between plant roots and soil bacteria. The aim of this study was to address the influences of tree species, tree species diversity and leaf litter on soil bacterial diversity and community composition. Therefore, mesocosm experiments using beech, ash, lime, maple and hornbeam were established in 2006, and sampled in October 2008 and June 2009. Mesocosms were planted with one, three or five different tree species and treated with or without litter overlay.Cluster analysis of DGGE-derived patterns revealed a clustering of 2008 sampled litter treatments in two separated clusters. The corresponding treatments sampled in 2009 showed separation in one cluster. PCA analysis based on the relative abundance of active proteobacterial classes and other phyla in beech and ash single-tree species mesocosm indicated an effect of sampling time and leaf litter on active bacterial community composition. The abundance of next-generation sequencing-derived sequences assigned to the Betaproteobacteria was higher in the litter treatments, indicating a higher activity, under these conditions. The Deltaproteobacteria, Nitrospira and Gemmatimonadetes showed an opposite trend and were more active in the mesocosms without litter. The abundance of alphaproteobacterial sequences was higher in mesocosms sampled in 2009 (P = 0.014), whereas the Acidobacteria were more active in 2008 (P = 0.014). At the family level, we found significant differences of the litter vs. non-litter treated group. Additionally, an impact of beech and ash as tree species on soil bacterial diversity was confirmed by the Shannon and Simpson indices. Our results suggest that leaf litter decomposition in pH-stable soils affect the soil bacterial composition, while tree species influence the soil bacterial diversity.     

Comparative diversity and abundance of ammonia monooxygenase genes in mulched and vegetated soils

Soil microbial habitats are altered by mulching, a common practice in urban areas during which vegetation is removed and soils covered to suppress weeds and retain moisture. Soil microorganisms drive nitrogen-cycling processes in mulched soils, because living plants no longer take up ammonium-N released during decomposition of residual organic matter. Because ammonia oxidizers carry out the first, rate-limiting step of nitrification, we compared ammonia oxidizers in experimental, unfertilized plots of mulched and vegetated soils. We hypothesized that mulched and vegetated soils would support contrasting communities of bacterial and archaeal ammonia oxidizers, as determined by quantitative PCR and primers specific for genes encoding ammonia monooxygenase subunit A (amoA). Clone libraries of archaeal amoA also were constructed to compare diversity in soil cores, duplicate blocked plots, and treatments (bark-mulched, gravel-mulched, and unmanaged old field vegetation). Gene copies from ammonia-oxidizing bacteria (AOB) ranged from 2.2 × 10⁶ to 2.7 × 10⁷ gene copies per gram dry soil and did not differ across treatments. In contrast, gene copies from ammonia-oxidizing archaea (AOA) ranged from 9.1 × 10⁵ to 1.0 × 10⁸ copies per gram dry soil, with bark-mulched soils having significantly lower abundance. Community structure of AOA in gravel-mulched soils was distinct from the other two treatments. At 97% amino acid similarity, 22 operational taxonomic units, or OTUs, were identified, with only one OTU found in all 18 clone libraries. This ubiquitous OTU-1, which was highly similar to published amoA sequences recovered from soils, comprised 55% of all 482 translated sequences. Greater variability in OTU richness was observed among cores from mulched soils than from vegetated soils. Our observations supported our hypothesis that AOA communities differ in mulched and vegetated soils, with mulched soils providing altered and variable microniches for these N cycling microorganisms.     

Inferring biological soil crust successional stage using combined PLFA, DGGE, physical and biophysiological analyses

Arid areas are highly sensitive to climate change and are ideal model systems to study the potential impact of climate change on species' community structure. Biological soil crust (BSC) formation plays an ecological role in a number of key processes in the development of dry ecosystems. It was hypothesized that BSC succession and function are affected by aridity level and limited by rainfall. Furthermore, it is possible to infer the direction of the BSC succession based on aridity level, and the latter can imitate future climate change scenarios. The objectives of this study were to investigate the microbial biomass and diversity of the BSC structure in three sites differing in aridity level (semiarid, arid and hyper-arid), by combining physical and biophysiological measurements with 16S rRNA gene fragment and phospholipid fatty acid (PLFA) analyses. Physical and biophysiological parameters of the BSC were significantly influenced by aridity level. Total protein and polysaccharide contents were strongly correlated with total PLFA-based microbial biomass. Gram-positive biomarkers and microbial biomass were significantly higher in the wettest (semiarid) site than in the driest (hyper-arid) one. Multivariate-analysis based ordination of the PLFA data segregated the cluster of semiarid data from that of the hyper-arid site, while data from the arid site were dispersed between the two. The phylogenetic distribution of prominent 16S rRNA bacterial gene sequences along the aridity levels was in agreement with the PLFA analysis: the hyper-arid site was dominated by the cyanobacterium Microcoleus vaginatus, while diverse populations of cyanobacteria and soil bacteria were found in the other sites. These complementary tools allowed a simple and sensitive measurement of the influence of aridity levels on BSC successional stage. The results demonstrate that different aridity levels correspond to different BSC successional stages and those differences can be used as parameters for global change scenarios.     

Incongruous variation of denitrifying bacterial communities as soil N level rises in Canadian canola fields

Soil N fertilization stimulates the activity of the soil bacterial species specialized in performing the different steps of the denitrification processes. Different responses of these bacterial denitrifiers to soil N management could alter the efficiency of reduction of the greenhouse gas N₂O into N₂ gas in cultivated fields. We used next generation sequencing to show how raising the soil N fertility of Canadian canola fields differentially modifies the diversity and composition of nitrite reductase (nirK and nirS) and nitrous oxide reductase (nosZ) gene-carrying denitrifying bacterial communities, based on a randomized complete blocks field experiment. Raising soil N levels increased up to 60% the ratio of the nirK to nirS genes, the two nitrite reductase coding genes, in the Brown soil and up to 300% in the Black soil, but this ratio was unaffected in the Dark Brown soil. Raising soil N levels also increased the diversity of the bacteria carrying the nitrite reductase gene nirK (Simpson index, P = 0.0417 and Shannon index, 0.0181), and changed the proportions of the six dominant phyla hosting nirK, nirS, and nosZ gene-carrying bacteria. The level of soil copper (Cu) and the abundance of nirK gene, which codes for a Cu-dependent nitrite reductase, were positively related in the Brown (P = 0.0060, R² = 0.48) and Dark Brown (0.0199, R² = 0.59) soils, but not in the Black soil. The level of total diversity of the denitrifying communities tended to remain constant as N fertilization induced shifts in the composition of these denitrifying communities. Together, our results indicate that higher N fertilizer rate increases the potential risk of nitrous oxide (N₂O) emission from canola fields by promoting the proliferation of the mostly adaptive N₂O-producing over the less adaptive N₂O-reducing bacterial community.     

Effect of agricultural land use change on community composition of bacteria and ammonia oxidizers

Purpose

Soil microbial communities can be strongly influenced by agricultural practices, but little is known about bacterial community successions as land use changes. The objective of this study was to determine microbial community shifts following major land use changes in order to improve our understanding of land use impacts on microbial community composition and functions.

Materials and methods

Four agricultural land use patterns were selected for the study, including old rice paddy fields (ORP), Magnolia nursery planting (MNP), short-term vegetable (STV), and long-term vegetable (LTV) cultivation. All four systems are located in the same region with same soil parent material (alluvium), and the MNP, STV, and LTV systems had been converted from ORP for 10, 3, and 30 years, respectively. Soil bacteria and ammonia oxidizer community compositions were analyzed by 454 pyrosequencing and terminal restriction fragment length polymorphism, respectively. Quantitative PCR was used to determine 16S rRNA and amoA gene copy numbers.

Results and discussion

The results showed that when land use was changed from rice paddy to upland systems, the relative abundance of Chloroflexi increased whereas Acidobacteria decreased significantly. While LTV induced significant shifts of bacterial composition, MNP had the highest relative abundance of genera GP1, GP2, and GP3, which were mainly related to the development of soil acidity. The community composition of ammonia-oxidizing bacteria (AOB) but not ammonia-oxidizing archaea was strongly impacted by the agricultural land use patterns, with LTV inducing the growth of a single super predominant AOB group. The land use changes also induced significant shifts in the abundance of 16S rRNA and bacterial amoA genes, but no significant differences in the abundance of archaea amoA was detected among the four land use patterns. Soil total phosphorous, available phosphorous, NO₃ ^?, and soil organic carbon contents and pH were the main determinants in driving the composition of both bacteria and AOB communities.

Conclusions

These results clearly show the significant impact of land use change on soil microbial community composition and abundance and this will have major implications on the microbial ecology and nutrient cycling in these systems, some of which is unknown. Further research should be directed to studying the impacts of these microbial community shifts on nutrient dynamics in these agroecosystems so that improved nutrient management systems can be developed.