Biogeographic patterns of soil diazotrophic communities across six forests in the North America

Soil diazotrophs play important roles in ecosystem functioning by converting atmospheric N₂ into biologically available ammonium. However, the diversity and distribution of soil diazotrophic communities in different forests and whether they follow biogeographic patterns similar to macroorganisms still remain unclear. By sequencing nifH gene amplicons, we surveyed the diversity, structure and biogeographic patterns of soil diazotrophic communities across six North American forests (126 nested samples). Our results showed that each forest harboured markedly different soil diazotrophic communities and that these communities followed traditional biogeographic patterns similar to plant and animal communities, including the taxa–area relationship (TAR) and latitudinal diversity gradient. Significantly higher community diversity and lower microbial spatial turnover rates (i.e. z‐values) were found for rainforests (~0.06) than temperate forests (~0.1). The gradient pattern of TARs and community diversity was strongly correlated (r² > 0.5) with latitude, annual mean temperature, plant species richness and precipitation, and weakly correlated (r² < 0.25) with pH and soil moisture. This study suggests that even microbial subcommunities (e.g. soil diazotrophs) follow general biogeographic patterns (e.g. TAR, latitudinal diversity gradient), and indicates that the metabolic theory of ecology and habitat heterogeneity may be the major underlying ecological mechanisms shaping the biogeographic patterns of soil diazotrophic communities.     

Decreasing Nitrogen Fertilizer Input Had Little Effect on Microbial Communities in Three Types of Soils

In this study, we examined the influence of different nitrogen (N) application rates (0, 168, 240, 270 and 312 kg N ha^-1) on soil properties, maize (Zea mays L.) yields and microbial communities of three types of soils (clay, alluvial and sandy soils). Phospholipid fatty acid analysis was used to characterize soil microbial communities. Results indicated that N fertilization significantly decreased microbial biomass in both clay and sandy soils regardless of application rate. These decreases were more likely a result of soil pH decreases induced by N fertilization, especially in the sandy soils. This is supported by structural equation modeling and redundancy analysis results. Nitrogen fertilization also led to significant changes in soil microbial community composition. However, the change differences were gradually dismissed with increase in N application rate. We also observed that N fertilization increased maize yields to the same level regardless of application rate. This suggests that farmers could apply N fertilizers at a lower rate (i.e. 168 kg N ha^-1), which could achieve high maize yield on one hand while maintain soil microbial functions on the other hand.     

Plant Functional Type Effects on Trace Gas Fluxes in the Shortgrass Steppe

Plant community structure is expected to regulate the microbial processes of nitrification and denitrification by controlling the availability of inorganic N substrates. Thus it could also be a factor in the concomitant release of NO and N2O from soils as a result of these processes. C3 and C4 plants differ in several attributes related to the cycling of nitrogen and were hypothesized to yield differences in trace gas exchange between soil and atmosphere. In this study we estimated fluxes of NO, N2O and CH4 from soils of shortgrass steppe communities dominated by either C3 plants, C4 plants or mixtures of the two types. We collected gas samples weekly from two sites, a sandy clay loam and a clay, throughout the growing seasons of 1995 and 1996. Plant functional type effects on gas fluxes at the clay site were not apparent, however we found several differences among plant communities on the sandy clay loam. CH4 uptake from atmosphere to soil was significantly greater on C4 plots than C3 plots in both years. NO fluxes were significantly greater from C4 plots than from C3 plots in 1995. NO fluxes from C3 and mixed plots were not significantly different between 1995 and 1996, however fluxes from C4 plots were significantly greater in 1995 compared to 1996. Results indicate that under certain environmental conditions, particularly when factors such as moisture and temperature are not limiting, plant community composition can play an important role in regulating trace gas exchange.     

Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes

The severe environmental stresses of the Arctic may have promoted unique soil bacterial communities compared with those found in lower latitude environments. Here, we present a comprehensive analysis of the biogeography of soil bacterial communities in the Arctic using a high resolution bar‐coded pyrosequencing technique. We also compared arctic soils with soils from a wide range of more temperate biomes to characterize variability in soil bacterial communities across the globe. We show that arctic soil bacterial community composition and diversity are structured according to local variation in soil pH rather than geographical proximity to neighboring sites, suggesting that local environmental heterogeneity is far more important than dispersal limitation in determining community‐level differences. Furthermore, bacterial community composition had similar levels of variability, richness and phylogenetic diversity within arctic soils as across soils from a wide range of lower latitudes, strongly suggesting a common diversity structure within soil bacterial communities around the globe. These results contrast with the well‐established latitudinal gradients in animal and plant diversity, suggesting that the controls on bacterial community distributions are fundamentally different from those observed for macro‐organisms and that our biome definitions are not useful for predicting variability in soil bacterial communities across the globe.     

Distribution of Extensive nifH Gene Diversity Across Physical Soil Microenvironments

The diversity of nitrogen-fixing bacteria is well described for aquatic environments; however, terrestrial analyses remain mostly biased to rhizobial plant–microbe associations. We maximized the level of resolution for this study through the use of nucleotide sequence information extracted from a series of soil microenvironments, ranging from macroaggregates at 2000 μm to the clay fraction at <75 μm in diameter. In addition, we attempted to create an overview of the distribution of terrestrial nitrogen fixers across such microenvironments by combining culture-independent techniques with a suite of natural soil environments from uniquely different origins. Soil diazotroph diversity was analyzed phylogenetically for 600 terrestrial nifH sequences from 12 midsized clone libraries based on microenvironments of three separate soils across a global scale. Statistical analyses of nifH gene clone libraries were used to estimate coverage, establish degrees of sequence overlap, and compare cluster distributions. These analyses revealed an extensive diversity in a tropical (19 phylotypes) and an arctic soil (17 phylotypes), and moderate diversity in a temperate soil (11 phylotypes). Within each soil, comparisons across aggregate size fractions delineated nifH gene cluster shifts within populations and degrees of sequence overlap that ranged from significantly different (arctic, tropical) to significantly similar (temperate). We suggest that this is due to population separation across aggregates of different size classes, which results from differences in the temporal stability of aggregates as niches for microbial communities. This study not only provides new knowledge of the arrangement of diazotrophic communities at the soil microscale, but it also contributes to the underrepresented knowledge of soil nifH sequences in the public databases.     

粉粒氨氮和水分影响浮霉菌门群落的空间分化

【背景】来自浮霉菌门(Planctomycetes)的厌氧氨氧化菌是高氨污染系统安全脱氮的生态友好型微生物,但关于特定生态梯度下Planctomycetes群落结构功能的空间分化以及驱动分化的主要环境因子等问题尚未引起关注。【目的】阐明Planctomycetes群落结构空间分化及影响其分化的主要环境因子。【方法】运用16S rRNA基因高通量测序手段检测温带半干旱区河流系统砂质及粉质沉积物、粉砂质及粉质土壤Planctomycetes群落结构的空间分布变化,统计学方法分析粉粒等理化因子对Planctomycetes群落结构功能分化的影响。【结果】OM190_ub_o_o. o1种群主要分布在寡营养的砂质沉积物中,仅由砂粒正向驱动;OM190_o_o_o. o2和SM1A02. ub5种群主要分布在中营养的粉砂质土壤中,由水分和pH等正向驱动;AKYG587.ub3、Pla4_lineage_o_o_o.o6、Singulisphaerao7、Singulisphaeraub8、Planctomycetaceae_u. ub9种群主要分布在全营养粉质土壤中,由黏粒、粉粒、盐度、有机碳、全氮、全磷、硝态氮正向驱动;Phycisphaera ub4种群虽优先分布在中营养的粉砂质土壤中,但表现出由中营养向全营养过渡的分布趋势,由硝态氮负向驱动;全部种群都由氨氮负向驱动。变异分析表明粉粒、氨氮、水分贡献了Planctomycetes群落结构变化52.7%、10.4%、10.3%的变异度。【结论】温带半干旱区河流系统Planctomycetes群落存在明显的空间分化特征,沉积物/土壤粉粒、氨氮和水分是驱动Planctomycetes群落结构及功能变异的主要因子,全营养粉质土壤中的Planctomycetes群落可能为附着型异养反硝化菌,寡营养粉砂质土壤中的Planctomycetes群落可能为对氨氮及硝态氮有高度亲和力的游离型自养氨氧化或反硝化菌,这为氨氧化或反硝化相关Planctomycetes群落高效应用于高氨等污染系统的生物脱氮提供了科学依据。     

Soil nutrient dynamics and community boundaries in the Fynbos vegetation of South Africa

The relationship between changes in soil nutrient characteristics and fynbos community boundaries was investigated near Cape Agulhas, South Africa. Soil characteristics relating to total nutrient content (pH, total N and total P, organic carbon, and various cations) were assessed at sites along three transects crossing the boundaries between five plant communities. Dynamics of available N and P in soils of three communities were studied in the field over one year, using ion-exchange resins. There was a wide range in the degree of change in soil nutrient content across different community boundaries. The characteristics that varied most were pH, total N, Ca and total P. Differences in available nutrients among soils indicated that the communities in this landscape were associated with a mosaic of N and P availability. It is proposed that spatial variation in soil nutrient availability rather than total soil nutrient contents may be important in explaining landscape-level species distributions and community composition in nutrient-poor mediterranean-climate ecosystems.     

Impacts of Organic and Conventional Crop Management on Diversity and Activity of Free-Living Nitrogen Fixing Bacteria and Total Bacteria Are Subsidiary to Temporal Effects

A three year field study (2007–2009) of the diversity and numbers of the total and metabolically active free-living diazotophic bacteria and total bacterial communities in organic and conventionally managed agricultural soil was conducted using the Nafferton Factorial Systems Comparison (NFSC) study, in northeast England. Fertility management appeared to have little impact on both diazotrophic and total bacterial communities. However, copy numbers of the nifH gene did appear to be negatively impacted by conventional crop protection measures across all years suggesting diazotrophs may be particularly sensitive to pesticides. Impacts of crop management were greatly overshadowed by the influence of temporal effects with diazotrophic communities changing on a year by year basis and from season to season. Quantitative analyses using qPCR of each community indicated that metabolically active diazotrophs were highest in year 1 but the population significantly declined in year 2 before recovering somewhat in the final year. The total bacterial population in contrast increased significantly each year. It appeared that the dominant drivers of qualitative and quantitative changes in both communities were annual and seasonal effects. Moreover, regression analyses showed activity of both communities was significantly affected by soil temperature and climatic conditions.     

Vegetation-Associated Impacts on Arctic Tundra Bacterial and Microeukaryotic Communities

The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO₂ concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith''s phylogenetic diversity, and the Shannon species-level index (H′) were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith''s phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure.     

Microbial Community Succession in an Unvegetated,Recently Deglaciated Soil

Primary succession is a fundamental process in macroecosystems; however, if and how soil development influences microbial community structure is poorly understood. Thus, we investigated changes in the bacterial community along a chronosequence of three unvegetated, early successional soils (∼20-year age gradient) from a receding glacier in southeastern Peru using molecular phylogenetic techniques. We found that evenness, phylogenetic diversity, and the number of phylotypes were lowest in the youngest soils, increased in the intermediate aged soils, and plateaued in the oldest soils. This increase in diversity was commensurate with an increase in the number of sequences related to common soil bacteria in the older soils, including members of the divisions Acidobacteria, Bacteroidetes, and Verrucomicrobia. Sequences related to the Comamonadaceae clade of the Betaproteobacteria were dominant in the youngest soil, decreased in abundance in the intermediate age soil, and were not detected in the oldest soil. These sequences are closely related to culturable heterotrophs from rock and ice environments, suggesting that they originated from organisms living within or below the glacier. Sequences related to a variety of nitrogen (N)-fixing clades within the Cyanobacteria were abundant along the chronosequence, comprising 6–40% of phylotypes along the age gradient. Although there was no obvious change in the overall abundance of cyanobacterial sequences along the chronosequence, there was a dramatic shift in the abundance of specific cyanobacterial phylotypes, with the intermediate aged soils containing the greatest diversity of these sequences. Most soil biogeochemical characteristics showed little change along this ∼20-year soil age gradient; however, soil N pools significantly increased with soil age, perhaps as a result of the activity of the N-fixing Cyanobacteria. Our results suggest that, like macrobial communities, soil microbial communities are structured by substrate age, and that they, too, undergo predictable changes through time.     

Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem

Alterations in soil bacterial communities across a transect between a semi natural upland grassland and an agriculturally improved enclosure were assessed using culture-based methods and a nucleic-acid-based method, terminal restriction fragment length polymorphism (TRFLP). While plant diversity decreased across the transect towards the improved area, numbers of 16S rDNA terminal restriction fragments increased, indicating an increase in numbers of bacterial ribotypes. Bacterial numbers, microbial activity, and potential functional diversity also followed a similar trend, increasing with decreasing plant diversity. Alterations in bacterial community structure were coincident with changes in soil physicochemical properties which also changed across the transect. Increases in soil pH, nitrate, phosphorus, potassium, and calcium occurred toward the improved grassland, while organic matter and ammonium declined. The inverse relationship between floristic diversity and bacterial ribotype numbers suggests that soil physicochemical factors may be as influential in determining bacterial diversity in soils of upland grassland communities as floristic diversity.     

湖南稻田土壤固定态铵含量的季节变化及生物有效性

以湖南省3种固定态铵含量较高的稻田土壤为供试土壤,通过盆栽试验,研究了稻田土壤固定态铵在植稻期间的动态变化及其生物有效性。结果表明,稻田土壤的固定态铵含量处于不断的变化之中,施氮肥和有机肥使土壤固定态铵含量升高,而水稻吸收氮则使土壤固定态铵含量降低,其变化趋势与土壤碱解氮含量变化相似。“新固定的”固定态铵基本对当季水稻全部有效。而“原有的”固定态铵对当季作物和后季作物部分有效,就供试土壤而言,在水稻生育期间,土壤固定态铵的释放量是潮沙泥>紫泥田>河沙泥;就不同水稻而言,早稻生育期间土壤固定态铵的释放量大于晚稻生育期间土壤固定态铵的释放量。     

Nitrogen uptake strategies of edaphically specialized Bornean tree species

The association of tree species with particular soil types contributes to high β diversity in forests, but the mechanisms producing such distributions are still debated. Soil nitrogen (N) often limits growth and occurs in differentially available chemical forms. In a Bornean forest where tree species composition changes dramatically along a soil gradient varying in supplies of different N-forms, we investigated whether tree species’ N-uptake and soil specialization strategies covaried. We analyzed foliar ¹⁵N natural abundance for a total of 216 tree species on clay or sandy loam (the soils at the gradient’s extremes) and conducted a ¹⁵N-tracer experiment with nine specialist and generalist species to test whether species displayed flexible or differential uptake of ammonium and nitrate. Despite variation in ammonium and nitrate supplies and nearly 4 ‰ difference in foliar δ¹⁵N between most soil specialists and populations of generalists on these soils, our ¹⁵N tracer experiment showed little support for the hypothesis that soil specialists vary in N-form use or the ratios in which they use these forms. Instead, our results indicate that these species possess flexible capacities to take up different inorganic N forms. Variation between soil specialists in uptake of different N forms is thus unlikely to cause the soil associations of tree species and high β diversity characteristic of this Bornean rain forest. Flexible uptake strategies would facilitate N-acquisition when supply rates of N-forms exhibit spatiotemporal variation and suggest that these species may be functionally redundant in their responses to N gradients and influences on ecosystem N-cycles.     

湖南主要类型稻田土壤固定态铵含量及其影响因素

通过野外调查取样和室内培养试验 ,应用Silva和Bremner方法 ,研究了湖南省主要类型稻田土壤的固定态铵含量及其影响因素 .结果表明 ,该省主要类型稻田土壤固定态铵含量为 141～ 35 3mg·kg-1,平均为 2 72± 6 7mg·kg-1,占土壤全N的 11.2 % ,高于湖南省以北各地区土壤和本地区地带性土壤———红壤的固定态铵含量 .其含量的顺序为河沙泥 >紫泥田 >潮沙泥 >黄泥田 >红黄泥 .在土壤剖面中 ,固定态铵含量随剖面深度的变化有 4种情况 :在 1m深度范围内随深度增加而增加 ;随深度增加而减少 ;随深度增加而无明显变化 ;土壤剖面中某一土层固定态铵含量明显增加或减少 .土壤固定态铵含量占土壤全N百分比随深度增加而恒增大 .土壤对NH+ 4的固定作用在 30℃下最强 ,高于 2 0℃和 40℃ ;长期淹水有利于潮沙泥、紫泥田和河沙泥对NH+ 4的固定作用 ,但干湿交替有利于黄泥田对NH+ 4的固定作用 .相关分析表明 ,土壤固定态铵含量仅与 <0 .0 1mm粘粒含量呈P0 .0 5水平的显著正相关 ,与有机质、全N、有机N和 <0 .0 0 1mm粘粒含量的相关性均不显著     

Fine root dynamics in relation to nutrients in oligotrophic Bornean rain forest soils

The fine roots of plants are key structures enabling soil resource acquisition, yet our understanding of their dynamics and the factors governing them is still underdeveloped, especially in tropical forests. We evaluated whether Bornean tree communities on soils with contrasting resource availability display different soil resource uptake strategies, based on their fine root properties and dynamics, and related responses of fine roots to the availability of multiple nutrients. Using root cores and ingrowth cores, we quantified variation in community-level fine root properties (biomass, length, and area) and their growth rates, biomass turnover rate, and specific root length (SRL) between clay and sandy loam soils, on which tree community composition differs dramatically. We found that standing fine root biomass and biomass, length, and area growth were higher in sandy loam, the soil type that is better-drained, coarser-textured, and less fertile for most nutrients. In clay SRL was significantly greater, and turnover tended to be faster, than in sandy loam. Across both soils, greater supplies of K⁺, NH₄ ⁺, and PO₄ ^3? were associated with greater standing biomass and growth rates of fine roots, suggesting foraging for these nutrients. Our data support the hypothesis that the sandy loam tree community achieves fine root absorptive area through faster growth and greater investment on a mass basis, whereas trees on clay achieve a similar standing absorptive area through slower growth of less-dense fine root tissues. Furthermore, our results suggest colimitation by multiple nutrients, which may enhance tree species coexistence through increased dimensionality of soil-resource niches.     

The Influence of Tropical Plant Diversity and Composition on Soil Microbial Communities

There is growing interest in understanding the linkages between above- and belowground communities, and very little is known about these linkages in tropical systems. Using an experimental site at La Selva Biological Station, Costa Rica, we examined whether plant diversity, plant community composition, and season influenced microbial communities. We also determined whether soil characteristics were related to differences in microbial communities. Phospholipid fatty acid (PLFA) composition revealed that microbial community composition differed across a plant diversity gradient (plots contained 1, 3, 5, or over 25 species). Plant species identity also was a factor influencing microbial community composition; PLFA composition significantly varied among monocultures, and among three-species combinations that differed in plant species composition. Differences among treatments within each of these comparisons were apparent in all four sampling dates of the study. There was no consistent shift in microbial community composition between wet and dry seasons, although we did see significant changes over time. Of all measured soil characteristics, soil C/N was most often associated with changes in microbial community composition across treatment groups. Our findings provide evidence for human alteration of soil microbial communities via the alteration of plant community composition and diversity and that such changes are mediated in part by changes in soil carbon quality.     

Microbial characteristics of sandy soils exposed to diazinon under laboratory conditions

Changes in microbiological characteristics in response to diazinon, applied at three different dosages of 7, 35 and 700 mg kg^?1 soil, were studied in pots filled with sandy soils of different texture. The insecticide dosages corresponded to the maximum predicted environmental concentration (PEC) in field conditions and five or hundred times this rate, respectively. To ascertain these changes, activities of selected soil enzymes, numbers of some microbial populations and bacterial community structure (r/K-strategists) were determined. Acid phosphatase activity and concentrations of ammonium ions either increased or were unaffected by the diazinon dosages. In contrast, nitrate ions, alkaline phosphatase, urease and especially dehydrogenase activities decreased in both soils treated with the higher dosages of the insecticide. The diazinon treatments increased the numbers of culturable bacteria and fungi; however, N-fixing bacteria and nitrifiers (but not denitrifiers) were decreased in both soils. When the high concentration of diazinon (100-times PEC) was added to the loamy sand soil (LS), simulating an undiluted chemical spill, the bacterial community structure shifted towards domination of K-strategists over time. However, r-strategists dominated in the community exposed to the same dosage of the insecticide in the sandy loam soil (SL). Generally, SL soil characteristics were more suitable for microbial activity and growth than those of LS soil were. The results indicate that except a situation of undiluted spill diazinon seems to be a non-hazardous chemical for the culturable soil microorganisms when applied at recommended concentrations.     

Environmental and plant community determinants of species loss following nitrogen enrichment

Global energy use and food production have increased nitrogen inputs to ecosystems worldwide, impacting plant community diversity, composition, and function. Previous studies show considerable variation across terrestrial herbaceous ecosystems in the magnitude of species loss following nitrogen (N) enrichment. What controls this variation remains unknown. We present results from 23 N-addition experiments across North America, representing a range of climatic, soil and plant community properties, to determine conditions that lead to greater diversity decline. Species loss in these communities ranged from 0 to 65% of control richness. Using hierarchical structural equation modelling, we found greater species loss in communities with a lower soil cation exchange capacity, colder regional temperature, and larger production increase following N addition, independent of initial species richness, plant productivity, and the relative abundance of most plant functional groups. Our results indicate sensitivity to N addition is co-determined by environmental conditions and production responsiveness, which overwhelm the effects of initial community structure and composition.     

Comparative study of endophytic and endophytic diazotrophic bacterial communities across rice landraces grown in the highlands of northern Thailand

Communities of bacterial endophytes within the rice landraces cultivated in the highlands of northern Thailand were studied using fingerprinting data of 16S rRNA and nifH genes profiling by polymerase chain reaction–denaturing gradient gel electrophoresis. The bacterial communities’ richness, diversity index, evenness, and stability were varied depending on the plant tissues, stages of growth, and rice cultivars. These indices for the endophytic diazotrophic bacteria within the landrace rice Bue Wah Bo were significantly the lowest. The endophytic bacteria revealed greater diversity by cluster analysis with seven clusters compared to the endophytic diazotrophic bacteria (three clusters). Principal component analysis suggested that the endophytic bacteria showed that the community structures across the rice landraces had a higher stability than those of the endophytic diazotrophic bacteria. Uncultured bacteria were found dominantly in both bacterial communities, while higher generic varieties were observed in the endophytic diazotrophic bacterial community. These differences in bacterial communities might be influenced either by genetic variation in the rice landraces or the rice cultivation system, where the nitrogen input affects the endophytic diazotrophic bacterial community.