Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils

Molecular approaches have revealed considerable diversity and uncultured novelty in natural prokaryotic populations, but not direct links between the new genotypes detected and ecosystem processes. Here we describe the influence of the structure of communities of ammonia-oxidizing bacteria on nitrogen cycling in microcosms containing natural and managed grasslands and amended with artificial sheep urine, a major factor determining local ammonia concentrations in these environments. Nitrification kinetics were assessed by analysis of changes in urea, ammonia, nitrite and nitrate concentrations and ammonia oxidizer communities were characterized by analysis of 16S rRNA genes amplified from extracted DNA using ammonia oxidizer-specific primers. In natural soils, ammonia oxidizer community structure determined the delay preceding nitrification, which depended on the relative abundance of two Nitrosospira clusters, termed 3a and 3b. In batch cultures, pure culture and enrichment culture representatives of Nitrosospira 3a were sensitive to high ammonia concentration, while Nitrosospira cluster 3b representatives and Nitrosomonas europaea were tolerant. Delays in nitrification occurred in natural soils dominated by Nitrosospira cluster 3a and resulted from the time required for growth of low concentrations of Nitrosospira cluster 3b. In microcosms dominated by Nitrosospira cluster 3b and Nitrosomonas, no substantial delays were observed. In managed soils, no delays in nitrification were detected, regardless of initial ammonia oxidizer community structure, most probably resulting from higher ammonia oxidizer cell concentrations. The data therefore demonstrate a direct link between bacterial community structure, physiological diversity and ecosystem function.     

Effects of long-term fertilization of forest soils on potential nitrification and on the abundance and community structure of ammonia oxidizers and nitrite oxidizers

Forest fertilization in British Columbia is increasing, to alleviate timber shortfalls resulting from the mountain pine beetle epidemic. However, fertilization effects on soil microbial communities, and consequently ecosystem processes, are poorly understood. Fertilization has contrasting effects on ammonia-oxidizing bacteria and archaea (AOB and AOA) in grassland and agricultural ecosystems, but there are no studies on AOB and AOA in forests. We assessed the effect of periodic (6-yearly application 200 kg N ha?1) and annual (c. 75 kg N ha?1) fertilization of lodgepole pine and spruce stands at five long-term maximum productivity sites on potential nitrification (PN), and the abundance and diversity of AOB, AOA and Nitrobacter and Nitrospira-like nitrite-oxidizing bacteria (NOB). Fertilization increased AOB and Nitrobacter-like NOB abundances at some sites, but did not influence AOA and Nitrospira-like NOB abundances. AOB and Nitrobacter-like NOB abundances were correlated with PN and soil nitrate concentration; no such correlations were observed for AOA and Nitrospira-like NOB. Autotrophic nitrification dominated (55–97%) in these forests and PN rates were enhanced for up to 2 years following periodic fertilization. More changes in community composition between control and fertilized plots were observed for AOB and Nitrobacter-like NOB than AOA. We conclude that fertilization causes rapid shifts in the structure of AOB and Nitrobacter-like NOB communities that dominate nitrification in these forests.     

长期施加氮肥及氧化钙调节对酸性土壤硝化作用及氨氧化微生物的影响

以长期施加氮肥及添加氧化钙调节的酸性土壤为研究对象,运用定量PCR和DGGE技术,探讨了土壤氨氧化微生物及硝化作用对不同施肥处理及氧化钙调节的响应。长期施化学氮肥导致酸性土壤p H(KCl)值(3.35—3.47)和硝化潜势(0.02—0.14μg NO-2-N g-1土壤h-1)进一步降低,而添加Ca O后土壤酸化得以缓解(p H值4.10—4.46),土壤硝化潜势(0.22—0.34μg NO-2-N g-1土h-1)显著增加。同时,添加Ca O处理对氨氧化古菌(AOA)的群落结构无明显影响,但明显提高了各施肥处理土壤中氨氧化细菌(AOB)的群落多样性,加Ca O处理的土壤中,AOA的数量降低而AOB的数量增加。这些结果表明虽然酸性土壤中AOA在数量和活性上占主导优势,AOB在功能上冗余,但当添加Ca O后,AOA和AOB对环境变化迅速作出响应,并根据其不同的生态位需求重新分配优势地位,二者交替作用共同驱动酸性土壤硝化作用。     

长期不同施肥制度对水稻土氨氧化微生物数量和群落结构的影响

由氨氧化微生物驱动的氨氧化过程是硝化作用的限速步骤,在土壤氮素循环过程中扮演着重要角色.以湖南省宁乡县长达30 a定位试验水稻土壤为研究对象,采用荧光定量PCR和Illumina MiSeq高通量测序分析方法,以amoA基因为靶标,研究了4种施肥制度[不施肥(CK)、化肥(CF)、70%化肥+30%有机肥(CFM₁)和40%化肥+60%有机肥(CFM₂)]水稻土壤氨氧化微生物的数量和群落结构变化.结果表明: 不同施肥处理氨氧化古菌(AOA)和氨氧化细菌(AOB) amoA基因拷贝数分别为3.09×10⁷～8.37×10⁷和1.04×10⁷～7.03×10⁷ copies·g^-1干土.施肥显著提高了AOA和AOB数量,但处理CFM₂中AOB数量与CK差异不显著.有机肥配施比例对AOB群落α多样性指数的影响强于AOA,处理CFM₁中AOA群落的多样性指数(Shannon)和AOB群落的丰富度指数(ACE和Chao1)均显著高于CK.奇古菌门和泉古菌门是AOA群落的优势门类群,占AOA amoA基因总序列的83.4%;亚硝化螺菌属、environmental_samples_norank、Bacteria_unclassified和Nitrosomonadales_unclassified是AOB群落的优势属类群,占AOB amoA基因总序列的97.8%.维恩分析结果显示,有机肥配施比例对AOB群落操作分类单元(OTU)数量的影响强于AOA,但对各处理共有AOA和AOB amoA基因序列条数的影响均较小.冗余分析结果显示,不同施肥处理AOB群落结构差异强于AOA,且所有土壤理化性质均与AOA和AOB群落结构存在显著相关关系.综上可知:有机肥配施比例显著改变了AOA和AOB数量、多样性和群落结构,配施30%有机肥时,AOA群落的Shannon指数最高,AOB群落数量、ACE和Chao1指数均最高.研究结果可为进一步探讨农业系统中氨氧化微生物对不同施肥制度的响应机制及其在氮素转化中的作用提供科学依据.     

Impacts of organic and inorganic fertilizers on nitrification in a cold climate soil are linked to the bacterial ammonia oxidizer community

The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from −40 to 38°C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the opposite response was measured for AOB, leading to a six- to 60-fold reduction in AOA/AOB ratio. The community structure of AOA exhibited little variation across fertilization treatments, whereas the structure of the AOB community was highly responsive. PNR was correlated with community structure of AOB rather than that of AOA. Variation in the community structure of AOB was linked to soil pH, total carbon, and nitrogen contents induced by different long-term fertilization regimes. The results suggest that manure amendment establishes conditions which select for an AOB community type which recovers mineral fertilizer-suppressed soil nitrification.     

Links between archaeal community structure, vegetation type and methanogenic pathway in Alaskan peatlands

Although northern peatlands contribute significantly to natural methane emissions, recent studies of the importance and type of methanogenesis in these systems have provided conflicting results. Mechanisms controlling methanogenesis in northern peatlands remain poorly understood, despite the importance of methane as a greenhouse gas. We used 16S rRNA gene retrieval and denaturing gradient gel electrophoresis (DGGE) to analyse archaeal communities in 15 high-latitude peatland sites in Alaska and three mid-latitude peatland sites in Massachusetts. Archaeal community composition was analysed in the context of environmental, vegetation and biogeochemical factors characterized in a parallel study. Phylogenetic analysis revealed that Alaskan sites were dominated by a cluster of uncultivated crenarchaeotes and members of the families Methanomicrobiaceae and Methanobacteriaceae, which are not acetoclastic. Members of the acetoclastic family Methanosarcinaceae were not detected, whereas those of the family Methanosaetaceae were either not detected or were minor. These results are consistent with biogeochemical evidence that acetoclastic methanogenesis is not a predominant terminal decomposition pathway in most of the sites analysed. Ordination analyses indicated a link between vegetation type and archaeal community composition, suggesting that plants (and/or the environmental conditions that control their distribution) influence both archaeal community activity and dynamics.     

Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils.

Autotrophic ammonia oxidizer (AAO) populations in soils from native, tilled, and successional treatments at the Kellogg Biological Station Long-Term Ecological Research site in southwestern Michigan were compared to assess effects of disturbance on these bacteria. N fertilization effects on AAO populations were also evaluated with soils from fertilized microplots within the successional treatments. Population structures were characterized by PCR amplification of microbial community DNA with group-specific 16S rRNA gene (rDNA) primers, cloning of PCR products and clone hybridizations with group-specific probes, phylogenetic analysis of partial 16S rDNA sequences, and denaturing gradient gel electrophoresis (DGGE) analysis. Population sizes were estimated by using most-probable-number (MPN) media containing varied concentrations of ammonium sulfate. Tilled soils contained higher numbers than did native soils of culturable AAOs that were less sensitive to different ammonium concentrations in MPN media. Compared to sequences from native soils, partial 16S rDNA sequences from tilled soils were less diverse and grouped exclusively within Nitrosospira cluster 3. Native soils yielded sequences representing three different AAO clusters. Probes for Nitrosospira cluster 3 hybridized with DGGE blots from tilled and fertilized successional soils but not with blots from native or unfertilized successional soils. Hybridization results thus suggested a positive association between the Nitrosospira cluster 3 subgroup and soils amended with inorganic N. DGGE patterns for soils sampled from replicated plots of each treatment were nearly identical for tilled and native soils in both sampling years, indicating spatial and temporal reproducibility based on treatment.     

Links between the abundance and distribution of birds

The relationship between overall abundance, local abundance and distribution is examined for several taxonomic groups of birds in Britain Among closely-related species, all three measures were correlated those species with the highest overall numbers also had the highest local numbers and the widest distributions Within each group, the relationship between overall abundance and distribution was extremely tight (with all the species points close to the trend line) in plots of log distribution (numbers of 10 km squares occupied) against log numbers The pattern held in summer and winter, and in both resident and migratory species Moreover, species which, over a period of years, underwent marked change in status showed parallel changes in both breeding numbers and distribution, and followed the pattern found from comparisons between related species Conversely, species which changed little in numbers over a period of years also changed little in extent of distribution
An explanation of the findings is proposed, based on density-dependent growth of local numbers and dispersal The relevance of the findings to the limitation of geographical ranges is discussed The distributional extent of many species seems to depend primarily on their overall numbers, rather than vice versa     

Links between the structure of an Antarctic shallow-water community and ice-scour frequency

Ice is a major structuring force in marine and freshwater environments at high latitudes. Although recovery from scouring has been quantified in time, the frequency of scouring in the Antarctic has not. We placed grids of markers at 9–17 m depth at two sites, to study ice-scouring over 2 years at Adelaide island (Antarctic Peninsula). We quantified the time scale of scour frequencies, and linked this to community mortality, age and diversity. Markers were hit from zero to at least three times in 2 years. At the least disturbed site (South Cove) 24% of markers were destroyed per year, whereas in North Cove 60% of markers were destroyed. There were significant differences in scouring frequency between our two sites: a given area in North Cove was on average hit twice as often as one in South Cove. Compared with near shore environments elsewhere, faunas of both sites were characteristic of high disturbance regimes, exhibiting low percent cover, diversity, ages and a high proportion of pioneers. Aspects of the encrusting communities studied reflected the differences between site disturbance regimes. North Cove was scoured twice as often, and bryozoan communities there had half the number of species, two-thirds the space occupation and twice the mortality level of those in South Cove. Maximum age in North Cove bryozoans was also half that in South Cove. Although there are natural disturbance events that rival ice-scouring in either frequency or catastrophic power at lower latitudes, none do both nor across such a wide depth range. We suggest that ice scour effects on polar benthos are even more significant than the same magnitude of disturbance at lower latitudes as recovery rates of high latitude communities are very slow. Climate warming seems likely to increase iceloading of near shore polar waters, so that some of the worlds most intensely disturbed faunas may soon suffer even more disturbance.     

Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils

Rice paddy fields are characterized by regular flooding and nitrogen fertilization, but the functional importance of aerobic ammonia oxidizers and nitrite oxidizers under unique agricultural management is poorly understood. In this study, we report the differential contributions of ammonia-oxidizing archaea (AOA), bacteria (AOB) and nitrite-oxidizing bacteria (NOB) to nitrification in four paddy soils from different geographic regions (Zi-Yang (ZY), Jiang-Du (JD), Lei-Zhou (LZ) and Jia-Xing (JX)) that are representative of the rice ecosystems in China. In urea-amended microcosms, nitrification activity varied greatly with 11.9, 9.46, 3.03 and 1.43 μg NO₃⁻-N g⁻¹ dry weight of soil per day in the ZY, JD, LZ and JX soils, respectively, over the course of a 56-day incubation period. Real-time quantitative PCR of amoA genes and pyrosequencing of 16S rRNA genes revealed significant increases in the AOA population to various extents, suggesting that their relative contributions to ammonia oxidation activity decreased from ZY to JD to LZ. The opposite trend was observed for AOB, and the JX soil stimulated only the AOB populations. DNA-based stable-isotope probing further demonstrated that active AOA numerically outcompeted their bacterial counterparts by 37.0-, 10.5- and 1.91-fold in ¹³C-DNA from ZY, JD and LZ soils, respectively, whereas AOB, but not AOA, were labeled in the JX soil during active nitrification. NOB were labeled to a much greater extent than AOA and AOB, and the addition of acetylene completely abolished the assimilation of ¹³CO₂ by nitrifying populations. Phylogenetic analysis suggested that archaeal ammonia oxidation was predominantly catalyzed by soil fosmid 29i4-related AOA within the soil group 1.1b lineage. Nitrosospira cluster 3-like AOB performed most bacterial ammonia oxidation in the ZY, LZ and JX soils, whereas the majority of the ¹³C-AOB in the JD soil was affiliated with the Nitrosomona communis lineage. The ¹³C-NOB was overwhelmingly dominated by Nitrospira rather than Nitrobacter. A significant correlation was observed between the active AOA/AOB ratio and the soil oxidation capacity, implying a greater advantage of AOA over AOB under microaerophilic conditions. These results suggest the important roles of soil physiochemical properties in determining the activities of ammonia oxidizers and nitrite oxidizers.     

Amino acid abundance and proteolytic potential in North American soils

Studies of nitrogen (N) cycling have traditionally focused on N mineralization as the primary process limiting plant assimilation of N. Recent evidence has shown that plants may assimilate amino acids (AAs) directly, circumventing the mineralization pathway. However, the general abundance of soil AAs and their relative importance in plant N uptake remains unclear in most ecosystems. We compared the concentrations and potential production rates of AAs and NH₄ ⁺, as well as the edaphic factors that influence AA dynamics, in 84 soils across the United States. Across all sites, NH₄ ⁺ and AA-N comprised similar proportions of the total bioavailable N pool (~20%), with NO₃ ⁻ being the dominant form of extractable N everywhere but in tundra and boreal forest soils. Potential rates of AA production were at least comparable to those of NH₄ ⁺ production in all ecosystems, particularly in semi-arid grasslands, where AA production rates were six times greater than for NH₄ ⁺ (P < 0.01). Potential rates of proteolytic enzyme activity were greatest in bacteria-dominated soils with low NH₄ ⁺ concentrations, including many grassland soils. Based on research performed under standardized laboratory conditions, our continental-scale analyses suggest that soil AA and NH₄ ⁺ concentrations are similar in most soils and that AAs may contribute to plant and microbial N demand in most ecosystems, particularly in ecosystems with N-poor soils.     

施肥方式对干旱半干旱地区土壤氨氧化微生物数量和群落的影响

氨氧化是硝化作用的限速步骤,也是评估土壤氮循环和提高氮肥利用效率的重要指标。以内蒙古农牧业科学院旱作实验站长期定位实验为基础,通过实时荧光定量PCR和末端限制性片段长度多态性分析,研究了5种施肥方式（单施氮肥、单施有机肥、氮磷钾配施、有机无机配施和不施肥）对土壤氨氧化古菌（AOA）和氨氧化细菌（AOB）群落丰度、结构和活性的影响。结果表明：单施氮肥、氮磷钾肥配施以及有机无机肥配施均能显著提高AOB的丰度以及土壤硝化潜势。Nitrosospiria cluster 3a.1是不施肥土壤中主要的AOB种群,而施用氮肥后优势种群转变为Nitrosospiria cluster 3a.2。Nitrosospiria cluster 3b的比例在施用有机肥处理土壤中显著升高。在干旱半干旱地区,土壤pH和含水量是解释AOB群落结构变化的关键环境因子。AOA的丰度在单独施用氮肥处理中显著升高,但不同施肥方式对AOA的群落结构没有显著影响。     

Heavy-machinery traffic impacts methane emissions as well as methanogen abundance and community structure in oxic forest soils

Temperate forest soils are usually efficient sinks for the greenhouse gas methane, at least in the absence of significant amounts of methanogens. We demonstrate here that trafficking with heavy harvesting machines caused a large reduction in CH(4) consumption and even turned well-aerated forest soils into net methane sources. In addition to studying methane fluxes, we investigated the responses of methanogens after trafficking in two different forest sites. Trafficking generated wheel tracks with different impact (low, moderate, severe, and unaffected). We found that machine passes decreased the soils' macropore space and lowered hydraulic conductivities in wheel tracks. Severely compacted soils yielded high methanogenic abundance, as demonstrated by quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes, whereas these sequences were undetectable in unaffected soils. Even after a year after traffic compression, methanogen abundance in compacted soils did not decline, indicating a stability of methanogens here over time. Compacted wheel tracks exhibited a relatively constant community structure, since we found several persisting mcrA sequence types continuously present at all sampling times. Phylogenetic analysis revealed a rather large methanogen diversity in the compacted soil, and most mcrA gene sequences were mostly similar to known sequences from wetlands. The majority of mcrA gene sequences belonged either to the order Methanosarcinales or Methanomicrobiales, whereas both sites were dominated by members of the families Methanomicrobiaceae Fencluster, with similar sequences obtained from peatland environments. The results show that compacting wet forest soils by heavy machinery causes increases in methane production and release.     

Nitrogen mineralization and potential nitrification at different depths in acid forest soils

Yield decline of cereals grown in monoculture may be alleviated with alternative crop management strategies. Crop rotation and optimized tillage and fertilizer management can contribute to more sustainable food and fiber production in the long-term by increasing diversity, maintaining soil organic matter (SOM), and reducing adverse effects of excessive N application on water quality. We investigated the effects of crop sequence, tillage, and N fertilization on long-term grain production on an alluvial, silty clay loam soil in southcentral Texas. Crop sequences consisted of monoculture sorghum (Sorghum bicolor (L.) Moench,) wheat (Triticum aestivum L.), and soybean (Glycine max (L.) Merr), wheat/soybean double-crop, and rotation of sorghum with wheat/soybean. Grain yields tended to be lower with no tillage (NT) than with conventional tillage (CT) early in the study and became more similar after 11 years. Nitrogen fertilizer required to produce 95% to maximum sorghum yield was similar for monoculture and rotation upon initiation of the experiment and averaged 16 and 11 mg N g^-1 grain with NT and CT, respectively. After 11 years, however, the N fertilizer requirement became similar for both tillage regimes, but was greater in monoculture (17 mg N g^-1 grain) than in rotation (12 mg N g^-1 grain). Crop sequences with double-cropping resulted in greater land use efficiency because similar or lower amounts of N fertilizer were required to produce equivalent grain than with less intensive monoculture systems. These more intensive crop sequences produced more stover with higher N quality primarily due to the inclusion of soybean in the rotation. Large quantities of stover that remained on the soil surface with NT led to greater SOM content, which increased the internal cycling of nutrients in this soil. In southcentral Texas, where rainfall averages nearly 1000 mm yr^-1, more intensive cropping of sorghum, wheat, and soybean with moderate N fertilization using reduced tillage can increase grain production and potentially decrease N losses to the environment by cycling more N into the crop-SOM system.     

不同有机肥对土壤镉锌生物有效性的影响

在南方典型稻田设置连续4年施用猪粪、鸡粪、稻草的定位试验,监测施用不同有机肥条件下土壤及水稻植株镉(Cd)、锌(Zn)含量的变化,研究有机肥对土壤Cd、Zn活性及其交互作用的影响.结果表明: 施用有机肥(猪粪、鸡粪、稻草)对土壤全Cd、有效态Cd含量及Cd活性皆无显著影响,但有增加土壤Cd全量的趋势,且显著增加土壤全Zn、有效态Zn含量及Zn活性.施用猪粪、鸡粪、稻草皆可降低稻米Cd含量,降Cd效果为猪粪>鸡粪>稻草,猪粪处理水稻稻米、茎、叶Cd含量分别比对照下降37.5%、44.0%、36.4%;鸡粪处理水稻米、茎、叶Cd含量分别比对照下降22.5%、33.8%、22.7%;而稻草处理水稻米Cd含量比对照下降7.5%,但茎、叶Cd含量比对照分别增加8.2%、22.7%;施用猪粪、鸡粪降低稻米Cd含量主要是降低了水稻植株对土壤Cd的富集,而施用稻草则主要是降低了水稻茎Cd向稻米的转运.施用有机肥还增加了水稻茎Zn含量,施用猪粪、鸡粪、稻草的水稻茎Zn含量比单施化肥分别增加53.4%、41.2%、13.9%,但对水稻稻米、叶Zn含量无显著影响.Zn、Cd在土壤、植株茎中皆表现出显著的拮抗作用,土壤及水稻茎Zn含量的增加显著抑制了水稻米、茎、叶对Cd的吸收积累,且随土壤有效态Zn/Cd含量比值的增加,Zn、Cd竞争土壤吸附不是抑制水稻吸收积累Cd的主控因子,而Zn、Cd竞争吸收才是影响水稻吸收积累Cd的主控因子.     

Links between the species abundance distribution and the shape of the corresponding rank abundance curve

Species abundance distribution (SAD) is a classic topic of multispecies ecology. Different types of SAD may indicate specific environmental conditions. A possible way to present some properties of a theoretical or empirical SAD is the construction of a rank-abundance curve (RAC). With regard to the applicability of the RAC as a widely used indicator of the structure of a multispecies community and of the ecological status of its habitat, a basic question is the link between the type of SAD and the shape of the associated RAC. One of the simplest ways to characterize a RAC is to determine its concave and convex segments. However, none of ecological textbooks does give a clear-cut guideline concerning this issue. In the paper a connection is presented between some types of SAD and the convex and concave segments of the related RAC: including among others linearity for the geometric SAD (e.g. with communities in early stage of succession), convexity for the Zipf-Mandelbrot SAD (e.g. with communities with slow successional process), and convexity and then concavity with an inflexion point at approximately the mode of the associated histogram for the lognormal SAD (e.g. with climax, equilibrium communities). Our approach has the potential to improve and justify the use of RACs when searching for the determinants of community structure, initiating further studies in this field.