Microbial community composition in sediments resists perturbation by nutrient enrichment

Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply in our sampling locations, despite demonstrable and diverse nutrient-induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation.     

Effects of an invasive cattail species (Typha x glauca) on sediment nitrogen and microbial community composition in a freshwater wetland

Sediments from Cheboygan Marsh, a coastal freshwater wetland on Lake Huron that has been invaded by an emergent exotic plant, Typhaxglauca, were examined to assess the effects of invasion on wetland nutrient levels and sediment microbial communities. Comparison of invaded and uninvaded zones of the marsh indicated that the invaded zone showed significantly lower plant diversity, as well as significantly higher aboveground plant biomass and soil organic matter. The sediments in the invaded zone also showed dramatically higher concentrations of soluble nutrients, including greater than 10-fold higher soluble ammonium, nitrate, and phosphate, which suggests that Typhaxglauca invasion may be impacting the wetland's ability to remove nutrients. Terminal restriction fragment length polymorphism analyses revealed significant differences in the composition of total bacterial communities (based on 16S-rRNA genes) and denitrifier communities (based on nirS genes) between invaded and uninvaded zones. This shift in denitrifiers in the sediments may be ecologically significant due to the critical role that denitrifying bacteria play in removal of nitrogen by wetlands.     

反硝化基因工程菌株YP4S的构建及对污水除氮特性研究

从养殖场污泥中筛选出菌株YP4,经16S rDNA分子发育树的同源序列比对,确定为克雷伯什菌属(Klebsiella sp.)。由NCBI数据库查编码亚硝酸还原酶(Nir)的基因nirS序列,设计引物,以铜绿假单胞菌PAOI基因组DNA为模板,应用PCR技术扩增目的片段nirS,经过双酶切、克隆和转化,得到重组质粒pYP4S,然后转化野生菌株YP4,构建反硝化基因工程菌YP4S。菌株生长曲线测定表明,工程菌株YP4S与YP4的生长特性基本一致。工程菌株YP4S对模拟污水COD、TN、NH_4^+-N和NO_3^--N具有较高的去除率,YP4S与YP4相比,对NO_2^--N积累的减少量为(32.44±3.96)%,明显减少了NO_2^--N的积累。通过正交试验获得工程菌株YP4S在C/N=10、T=30℃、r=200 r/min和pH=7.0的最佳组合条件下,对模拟污水TN去除率较高。应用工程菌株YP4S处理猪场沉淀池的实际污水,COD、TN、TP、NH_4^+-N和NO_3^--N去除率分别为(95.87±0.82)%、(76.38±3.84)%、(97.13±0.54)%和(75.35±2.57)%,NO_2^--N积累量为(3.31±1.24) mg/L,表明工程菌株YP4S具有较好反硝化作用,对含氮量高的实际污水修复具有潜在的应用前景。     

固氮施氏假单胞菌亚硝酸盐还原酶基因nirS转录特性及功能鉴定

【目的】研究固氮施氏假单胞菌(Pseudomonas stutzeri)A1501亚硝酸盐还原酶结构基因nir S的转录调控机制及其在反硝化过程中的功能。【方法】构建nir S-lac Z融合载体,利用三亲本结合法将其导入野生型A1501,通过β-半乳糖苷酶活性的测定,分析不同供氧状况、不同浓度的硝酸盐、亚硝酸盐对nir S基因表达的影响;同时将该载体导入rpo N突变株中,研究氮代谢调控因子Rpo N对nir S基因转录影响。通过同源重组方法构建nir S突变株,通过生化表型测定明确nir S在反硝化过程中的功能。【结果】启动子活性测定表明,nir S基因厌氧条件下高水平表达,是好氧条件下表达水平的4倍;nir S的表达受硝酸盐诱导,但不受亚硝酸盐的诱导;Rpo N突变株中,nir S的表达活性为野生型的1/4,nir S启动子未发现Rpo N的保守结合位点,表明nir S的表达受Rpo N间接调控。表型测定显示以硝酸盐为电子受体时Δnir S的反硝化能力降低了约20%;以亚硝酸盐为电子受体时Δnir S仅有微弱的反硝化能力,并且nir S的突变使得菌体在反硝化条件下利用亚硝酸盐的能力显著减弱。nir S突变提高了菌体在亚硝酸为电子受体的反硝化条件下的固氮酶活。【结论】A1501中nir S基因的转录受外界氧及硝酸盐的影响,同时受氮代谢Sigma因子Rpo N的调控。nir S在A1501菌反硝化过程中起关键作用,参与了亚硝酸盐的转化。     

Does soil aging affect the N2O mitigation potential of biochar? A combined microcosm and field study

The application of biochar as a soil amendment to improve soil fertility has been suggested as a tool to reduce soil‐borne CO₂ and non‐CO₂ greenhouse gas emissions, especially nitrous oxide (N₂O). Both laboratory and field trials have demonstrated N₂O emission reduction by biochar amendment, but the long‐term effect (>1 year) has been questioned. Here, we present results of a combined microcosm and field study using a powdered beech wood biochar from slow pyrolysis. The field experiment showed that both CO₂ and N₂O emissions were still effectively reduced by biochar in the third year after application. However, biochar did not influence the biomass yield of sunflower for biogas production (Helianthus annuus L.). Biochar reduced bulk density and increased soil aeration and thus reduced the water‐filled pore space (WFPS) in the field, but was also able to suppress N₂O emission in the microcosms experiment conducted at constant WFPS. For both experiments, biochar had limited impact on soil mineral nitrogen speciation, but it reduced the accumulation of nitrite in the microcosms. Extraction of soil DNA and quantification of functional marker genes by quantitative polymerase chain reaction showed that biochar did not alter the abundance of nitrogen‐transforming bacteria and archaea in both field and microcosm experiments. In contradiction to previous experiments, this study demonstrates the long‐term N₂O emission suppression potential of a wood biochar and thus highlights its overall climate change mitigation potential. While a detailed understanding of the underlying mechanisms requires further research, we provide evidence for a range of biochar‐induced changes to the soil environment and their change with time that might explain the often observed N₂O emission suppression.     

典型对虾养殖水体中参与硝化与反硝化过程的微生物群落结构

【目的】本研究旨在分析典型虾塘养殖水体中参与氮循环关键过程的菌群多样性,为指导实际对虾养殖水体中NH 4+和NO 2-的微生物降解、水体氮素污染控制以及虾塘养殖氮素循环的有效管理提供科学依据。【方法】使用聚合酶链式反应及变性梯度凝胶电泳技术(Polymerase Chain Reaction-Denaturing Gradient GelElectrophoresis,PCR-DGGE)从8个不同地点的虾塘水样中确定代表性水样,以此为典型水样进行研究,构建了氨单加氧酶基因(amoA)、亚硝酸盐氧化还原酶基因(nxrA)、亚硝酸盐还原酶基因(nirS)的克隆文库。利用限制性片段长度多态性(Restriction Fragment Length Polymorphism,RFLP)技术将克隆文库进行酶切分析。【结果】通过序列多态性分析,表明amoA基因克隆文库中所有序列都属于变形杆菌门β亚纲(β-Proteobacteria),分别为亚硝化单细胞菌属(Nitrosomonas)(81%)和亚硝化螺旋菌属(Nitrosospira)(19%)2个属。nxrA基因克隆文库检测到α-Proteobacteria和δ-Proteobacteria两个亚纲,其中硝化杆菌属(Nitrobacter)是优势菌群,占整个文库的92%,仅有一个类群属于δ亚纲的脱硫杆菌科(Desulfobacteraceae)(8%)。nirS基因文库群落结构相对于amoA和nxrA基因文库较复杂,分别为α-Proteobacteria、β-Proteobacteria亚纲和Actinobacteria,序列分析表明,25%的类群为固氮弧菌属(Azoarcus),25%的类群为(Polymorphum),20%的类群为需氧去氮菌属(Thauera),10%的类群为(Sophophora),10%的的类群为链霉菌属(Streptomyces),5%的类群为(Brachymonas),5%的类群为(Ruegeria)。【结论】典型虾塘养殖水环境中氮素循环关键过程的菌群多样性丰富,其中亚硝化单胞菌属(Nitrosomonas)和硝化杆菌属(Nitrobacter)分别是此环境中主要的氨氧化作用推动者和亚硝酸盐氧化作用推动者,而在反硝化重要环节中,固氮弧菌属等多种菌群都起着推动作用。     

Identification of denitrifying rhizobacteria from bentgrass and bermudagrass golf greens

AIMS: As high rates of nitrogen fertilization are used in turfgrass management, there is a great potential for nitrogen loss. Research on identification of denitrifiers in turfgrass has been limited. Therefore, the aim was to identify denitrifier species and genes from turfgrass roots. METHODS AND RESULTS: Rhizobacteria were isolated from roots of bentgrass and bermudagrass in sand-based United States Golf Association (USGA) golf greens and used for denitrification biochemical analysis. Seventeen per cent (34 isolates) were identified as denitrifiers, 47% were classified as nitrate-reducers and 36% were nondenitrifiers. Identification of species of the denitrifiers was performed by chromatography fatty acid methyl ester (GC-FAME) and16S rDNA analyses. Bacillus and Pseudomonas were the major turfgrass denitrifiers. The two methods showed a 60% agreement at the genus level. Nitrite reductase genes nirK and nirS were detected in 74 and 15% of the denitrifiers, respectively, but not in nondenitrifiers. The nosZ gene encoding nitrous oxide reductase was detected in all the denitrifiers, but also in some nondenitrifiers. CONCLUSIONS: To our knowledge, this is the first report for identification of denitrifiers and denitrification-related genes associated with turfgrass roots. SIGNIFICANCE AND IMPACT OF THE STUDY: These results provide valuable data for future denitrification studies that seek to improve turfgrass nitrogen management for maximum efficiency.     

Can differences in microbial abundances help explain enhanced N2O emissions in a permanent grassland under elevated atmospheric CO2?

Long‐term effects of elevated atmospheric CO₂ on the ammonia‐oxidizing and denitrifying bacteria in a grassland soil were investigated to test whether a shift in abundance of these N‐cycling microorganisms was responsible for enhanced N₂O emissions under elevated atmospheric CO₂. Soil samples (7.5 cm increments to 45 cm depth) were collected in 2008 from the University of Giessen Free Air Carbon dioxide Enrichment (GiFACE), a permanent grassland exposed to moderately elevated atmospheric CO₂ (+20%) since 1998. GiFACE plots lay on a soil moisture gradient because of gradually changing depth to the underlying water table and labeled as the DRY block (furthest from water table), MED block (intermediate to water table), and WET block (nearest to water table). Mean N₂O emissions measured since 1998 have been significantly higher under elevated CO₂. This study sought to identify microbial and biochemical parameters that might explain higher N₂O emissions under elevated CO₂. Soil biochemical parameters [extractable organic carbon (EOC), dissolved organic nitrogen (DON), NH₄⁺, NO₃^?], and abundances of genes encoding the key enzymes involved in ammonia oxidation (amoA) and denitrification (nirK, nirS, nosZ) depended more on soil depth and block (underlying soil moisture gradient) than on elevated CO₂. Ammonia oxidation and denitrification gene abundances, relative abundances (ratios) of nirS to nirK, of nosZ to both nirS and to nirK, and of the measured soil biochemical properties DON and NO₃^? tended to be lower in elevated CO₂ plots as compared with ambient plots in the MED and WET blocks while the DRY block exhibited an opposite trend. High N₂O emissions under elevated CO₂ in the MED and WET blocks correlated with lower nosZ to nirK ratios, suggesting that increased N₂O emissions under elevated CO₂ might be caused by a higher proportion of N₂O‐producing rather than N₂O consuming (N₂ producing) denitrifiers.     

九龙江河口区nirS型反硝化细菌多样性及系统发育学分析

【目的】结合16S rRNA基因克隆文库和nirS基因克隆文库的分析,揭示九龙江河口区nirS型反硝化细菌多样性。【方法】选取九龙江河口区一富营养化采样点,分别采集水样及沉积物样品,进行理化因子的测定并提取细菌总DNA。以水样DNA构建16S rRNA基因克隆文库,以沉积物DNA构建nirS基因克隆文库,分析微生物群落结构的多样性并构建系统发育树。【结果】从16S rRNA基因克隆文库中获得86条有效序列,按97%的序列相似性划分为53个OTU,分别属于Proteobacteria门、Planctomycetes门、Bacteroidetes门、Actinobacteria门、Firmicutes门和Chloroflexi门。其中属于Proteobacteria门OTU的克隆子占克隆数的62.9%,是最优势的类群,分属于Alphaproteobacteria、Betaproteobacteria、Gammaproteobacteria和Deltaproteobacteria纲等。从nirS基因克隆文库中获得190条有效序列,翻译为氨基酸序列后,按82%的序列相似性划分为60个OTU,并定位到属的水平。其中Proteobacteria门是最优势的类群,占文库克隆子总数的71.6%,包括Alphaproteobacteria纲(5.8%)、Betaproteobacteria纲(49.0%)和Gammaproteobacteria纲(16.9%)。nirS基因克隆文库中丰度最高的OTU与GenBank中的一株可培养反硝化菌Thauera sp. R-26906具有100%的序列相似性。【结论】九龙江河口区的微生物以及亚硝酸盐还原酶基因(nirS)具有丰富的多样性。大部分NirS序列在GenBank中的最相似序列来源于河口、海湾等相似的环境。     

珠江口沉积物好氧反硝化细菌的筛选及鉴定

研究首次于珠江口沉积物中分离出多株好氧反硝化细菌,从中筛选出一株反硝化性能最强的菌株A14-1。综合其生理生化及分子生物学鉴定的结果确定此菌株为红球菌属Rhodococcus aetherivorar。此菌株可在48 h内将培养基中的硝酸盐含量从157.91mg·L^-1降低至32.07mg·L^-1,反硝化效率高达26.20 mg·L^-1·h^-1,且不会产生亚硝酸盐的明显积累。以细菌总基因组DNA为模板成功扩增出亚硝酸还原酶基因nirS,说明亚硝酸还原酶可能参与了此菌株的好氧反硝化过程,将亚硝酸盐进一步还原,从而不会造成水体亚硝酸盐的积累。菌株A14-1在珠江口多个站点均有分布,环境适应能力强,且不会对环境造成危害,因此有望应用于污水的生物脱氮处理中。