Changes of Diversity Pattern of Proteolytic Bacteria over Time and Space in an Agricultural Soil

The genetic heterogeneity of neutral metalloprotease (npr) gene fragments from soil proteolytic bacteria was investigated at a cultivated field site with four different soil types and at three different depths in April, July, and October. Terminal restriction fragment length polymorphism (T-RFLP) analyses of polymerase chain reaction-amplified npr gene fragments were applied to study the dynamic of the npr gene pool with regard to environmental conditions. The aim of this study was to relate differences in npr community structure and richness to the vertical, site, and seasonal variations naturally occurring at the field site under investigation. T-RFLP analysis revealed a noticeable seasonal variability in the community structure of npr-containing bacteria. The data suggest that the composition of the npr proteolytic bacterial population in July differed from those at the other dates. Additionally, the diversity of npr genes decreased with increasing soil depth revealing the highest values in upper layers. The reasons behind the observed patterns in the community structure might be mainly seasonal and vertical variation of the quantity and heterogeneity of available substrates as well as spatial isolation caused by a varying water amount and the connectivity of soil particles among the soil profile. Sequencing and phylogenetical analysis of 120 npr clones from the top soils collected in July revealed that most of the clones exhibit only poor homology to npr genes of isolates previously obtained from various environments, indicating the presence of until now uncharacterized npr coding proteolytic bacteria at the study site.     

Plant Species and Plant Incubation Conditions Influence Variability in Epiphytic Bacterial Population Size

Abstract The influences of plant species and plant incubation conditions on the variability in bacterial population sizes among leaves were investigated in field and growth chamber studies. Pseudomonas syringae strains TLP2 and Cit7 were inoculated onto plants and population sizes were measured at intervals after inoculation. Total bacterial population sizes were also assessed in field studies. Levels of leaf-to-leaf variability in both P. syringae population size and bacterial community size differed significantly among plant species. For all plant species, variability among leaves in population sizes of inoculated bacteria was consistently greater than the leaf-to-leaf variability in numbers of total bacteria. Considering levels of variability in population size immediately prior to and following incubation under either wet or dry physical conditions, leaf-to-leaf variability in the population sizes of inoculated P. syringae strains increased significantly following incubation under dry, but not under wet, conditions. Measurements of leaf-to-leaf variability immediately prior to and following incubation were positively correlated regardless of whether the incubation was under wet or dry conditions, though the correlation was greater following dry incubation. These data provide insight into the biological and physical factors that may be important in generating variability in bacterial population sizes among leaves, and they have important implications for the design of appropriate strategies for sampling leaf surface microbial populations.     

Fungal Diversity in Deep Sea Sediments from East Yap Trench and Their Denitrification Potential

Abstract

In recent years, the hadal trenches have been recognized as biological hot spots for deep sea researchers. Due to high hydrostatic pressure, low temperatures, high salinity and low nutrients, the microorganisms in hadal trenches may have unique community structure with potential for biotechnical application. Compared with bacteria and archaea, the diversity and ecological roles of fungi in hadal trenches remain largely unknown. The purpose of this study was to explore fungal diversity in deep-sea sediments of the Yap trench and their denitrification potential. In the present study, a total of 106 fungal strains were isolated from six sediment samples collected in the East Yap Trench. These fungi belonged to five classes (Dothideomycetes, Eurotiomycetes, Sordariomycetes, Cystobasidiomycetes, and Microbotryomycetes), thirteen genera (Acremonium, Alternaria, Aureobasidium, Aspergillus, Cladosporium, Cystobasidium, Engyodontium, Gliomastix, Lecanicillium, Penicillium, Phoma, Rhodotorula and Trichoderma) and eighteen species, based on morphological identification and ITS-rDNA sequence analysis. Among them, the dominant genus is Cladosporium, which accounting for 42.45% of the total fungal strains. Meanwhile, the denitrification potential of the fungal strains was also examined with two different denitrifying media (nitrate and nitrite as sole substrate, respectively). Two fungal strains (Acremonium sp. and Aspergillus versicolor), were found to be able to produce N₂O ex situ in the presence of nitrite. No fungus was found to produce N₂O by using nitrate. Our results suggest that fungi in hadal sediments, play important roles in nitrogen cycles.     

Soil Environmental Conditions and Microbial Build-Up Mediate the Effect of Plant Diversity on Soil Nitrifying and Denitrifying Enzyme Activities in Temperate Grasslands

Random reductions in plant diversity can affect ecosystem functioning, but it is still unclear which components of plant diversity (species number – namely richness, presence of particular plant functional groups, or particular combinations of these) and associated biotic and abiotic drivers explain the observed relationships, particularly for soil processes. We assembled grassland communities including 1 to 16 plant species with a factorial separation of the effects of richness and functional group composition to analyze how plant diversity components influence soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), the abundance of nitrifiers (bacterial and archaeal amoA gene number) and denitrifiers (nirK, nirS and nosZ gene number), and key soil environmental conditions. Plant diversity effects were largely due to differences in functional group composition between communities of identical richness (number of sown species), though richness also had an effect per se. NEA was positively related to the percentage of legumes in terms of sown species number, the additional effect of richness at any given legume percentage being negative. DEA was higher in plots with legumes, decreased with increasing percentage of grasses, and increased with richness. No correlation was observed between DEA and denitrifier abundance. NEA increased with the abundance of ammonia oxidizing bacteria. The effect of richness on NEA was entirely due to the build-up of nitrifying organisms, while legume effect was partly linked to modified ammonium availability and nitrifier abundance. Richness effect on DEA was entirely due to changes in soil moisture, while the effects of legumes and grasses were partly due to modified nitrate availability, which influenced the specific activity of denitrifiers. These results suggest that plant diversity-induced changes in microbial specific activity are important for facultative activities such as denitrification, whereas changes in microbial abundance play a major role for non-facultative activities such as nitrification.     

Plant Diversity Impacts Decomposition and Herbivory via Changes in Aboveground Arthropods

Loss of plant diversity influences essential ecosystem processes as aboveground productivity, and can have cascading effects on the arthropod communities in adjacent trophic levels. However, few studies have examined how those changes in arthropod communities can have additional impacts on ecosystem processes caused by them (e.g. pollination, bioturbation, predation, decomposition, herbivory). Therefore, including arthropod effects in predictions of the impact of plant diversity loss on such ecosystem processes is an important but little studied piece of information. In a grassland biodiversity experiment, we addressed this gap by assessing aboveground decomposer and herbivore communities and linking their abundance and diversity to rates of decomposition and herbivory. Path analyses showed that increasing plant diversity led to higher abundance and diversity of decomposing arthropods through higher plant biomass. Higher species richness of decomposers, in turn, enhanced decomposition. Similarly, species-rich plant communities hosted a higher abundance and diversity of herbivores through elevated plant biomass and C:N ratio, leading to higher herbivory rates. Integrating trophic interactions into the study of biodiversity effects is required to understand the multiple pathways by which biodiversity affects ecosystem functioning.     

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.     

生态养殖河田鸡对林下植被多样性及土壤的影响

通过林下人工种草养殖河田鸡,调查林下生态养殖区与对照区的林木蓄积量、林地植被多样性指标、土壤理化性状、土壤侵蚀性。结果显示,林下生态养殖区内林木蓄积量显著高于对照区(P0.05);植被多样性与对照相比差异不显著(P0.05);土壤含水量、土壤pH值、硝态氮和铵态氮与对照相比均有所提高;林下生态养殖区下坡位的土壤侵蚀模数为120 t·km~(-2),与对照区相比总体土壤侵蚀量下降770 t·km~(-2),降幅达95.1%。     

长湖水生植物多样性及其变化

研究了湖北省第三大湖泊长湖水生植物多样性的现状及其长期变化,并探讨了多样性丧失的机理及多样性恢复与保护的有效途径。主要结论：(1)长湖现有水生植物98种,多度最大的是微齿眼子菜(Potamogeton maackianus)、密齿苦草(Vallisneria denseserrulata)、野菱(Trapa incisa)、双角菱(T.bispinosa)、菹草(Potamogeton crispus)、紫萍(Spirodela polyrhiza)、穗花狐尾藻(Myriophyllum spicatum)、轮叶黑藻(Hydrilla verticillata)、满江红(Azolla imbricata)。(2)长湖现有水生植物群丛类型14个,群落物种多样性指数最高的是芡实 野菱 双角菱群丛(Euryale ferox Trapa incisa T.bispinosa Ass.),其次为轮叶黑藻 密齿苦草|大茨藻群丛(Hydrilla verticillata Vallisneria denseserrulata Najas marioa Ass.)与竹叶眼子菜 穗花狐尾藻群丛(Potamogeton malaianus Myriophylhum spicatum Ass.)。(3)20年来,已有6种水生植物和7个水生植物群丛类型从长湖消失,植被覆盖率下降了54．85％,全湖平均单位面积生物量下降了69．78％。(4)多样性丧失的主要原因是过度养殖、过度打草和耙捞作业,以及由此导致的湖水透明度的大幅度下降。(5)多样性恢复的有效途径是政府部门的行政干预与经济支持。     

Spatial and Temporal Variability in Sediment Denitrification Within an Agriculturally Influenced Reservoir

Reservoirs are intrinsically linked to the rivers that feed them, creating a river–reservoir continuum in which water and sediment inputs are a function of the surrounding watershed land use. We examined the spatial and temporal variability of sediment denitrification rates by sampling longitudinally along an agriculturally influenced river–reservoir continuum monthly for 13 months. Sediment denitrification rates ranged from 0 to 63 μg N₂O g ash free dry mass of sediments (AFDM)⁻¹ h⁻¹ or 0–2.7 μg N₂O g dry mass of sediments (DM)⁻¹ h⁻¹ at reservoir sites, vs. 0–12 μg N₂O gAFDM⁻¹ h⁻¹ or 0–0.27 μg N₂O gDM⁻¹ h⁻¹ at riverine sites. Temporally, highest denitrification activity traveled through the reservoir from upper reservoir sites to the dam, following the load of high nitrate (NO₃⁻-N) water associated with spring runoff. Annual mean sediment denitrification rates at different reservoir sites were consistently higher than at riverine sites, yet significant relationships among theses sites differed when denitrification rates were expressed per gDM vs. per gAFDM. There was a significant positive relationship between sediment denitrification rates and NO₃⁻-N concentration up to a threshold of 0.88 mg NO₃⁻ -N l⁻¹, above which it appeared NO₃⁻-N was no longer limiting. Denitrification assays were amended seasonally with NO₃⁻-N and an organic carbon source (glucose) to determine nutrient limitation of sediment denitrification. While organic carbon never limited sediment denitrification, all sites were significantly limited by NO₃⁻-N during fall and winter when ambient NO ₃⁻-N was low.     

Effects of Plant Biomass, Plant Diversity, and Water Content on Bacterial Communities in Soil Lysimeters: Implications for the Determinants of Bacterial Diversity

Soils may comprise tens of thousands to millions of bacterial species. It is still unclear whether this high level of diversity is governed by functional redundancy or by a multitude of ecological niches. In order to address this question, we analyzed the reproducibility of bacterial community composition after different experimental manipulations. Soil lysimeters were planted with four different types of plant communities, and the water content was adjusted. Group-specific phylogenetic fingerprinting by PCR-denaturing gradient gel electrophoresis revealed clear differences in the composition of Alphaproteobacteria, Betaproteobacteria, Bacteroidetes, Chloroflexi, Planctomycetes, and Verrucomicrobia populations in soils without plants compared to that of populations in planted soils, whereas no influence of plant species composition on bacterial diversity could be discerned. These results indicate that the presence of higher plant species affects the species composition of bacterial groups in a reproducible manner and even outside of the rhizosphere. In contrast, the environmental factors tested did not affect the composition of Acidobacteria, Actinobacteria, Archaea, and Firmicutes populations. One-third (52 out of 160) of the sequence types were found to be specifically and reproducibly associated with the absence or presence of plants. Unexpectedly, this was also true for numerous minor constituents of the soil bacterial assemblage. Subsequently, one of the low-abundance phylotypes (beta10) was selected for studying the interdependence under particular experimental conditions and the underlying causes in more detail. This so-far-uncultured phylotype of the Betaproteobacteria species represented up to 0.18% of all bacterial cells in planted lysimeters compared to 0.017% in unplanted systems. A cultured representative of this phylotype exhibited high physiological flexibility and was capable of utilizing major constituents of root exudates. Our results suggest that the bacterial species composition in soil is determined to a significant extent by abiotic and biotic factors, rather than by mere chance, thereby reflecting a multitude of distinct ecological niches.     

The Potential Impact of An Introduced Shrub on Native Plant Diversity and Forest Regeneration

Over a period of 20 years, Chinese privet, Ligustrum sinense, invaded a mixed hardwood forest in western North Carolina, USA. The invasion penetrated about 30m under the canopy trees, providing 100% cover of the forest floor. Under the privets and in a nearby privet-poor reference area we marked off twenty, one square meter plots with string. All plants in each square meter of both areas were tallied in the spring of 1999 and young trees less than 1m high were again counted in September. We removed privets of the invaded area in November and again tallied all plants in both areas the following spring of 2000. In the spring of 1999, the mean number of herb species per square meter under the privet was 41%, and stem counts 75% less than in the reference area. 42% of herb species found in the reference area were missing under the privet. After removing the privets in the fall of 1999, the number of both native species and stems increased in the privet area the following spring. Plots of density of two native plants against privet density showed both native plants decreasing under increasing privet cover. In the spring of 1999, there were 4 species and 274 stems of tree seedlings in the privet area. In September of that year, we found only one small American holly tree, a highly shade-tolerant species, remaining under the privet. Our data support the thesis that Chinese privet can severely reduce herbaceous species and almost completely suppress tree regeneration in a mixed hardwood forest.     

Substrate Induced Denitrification over or under Estimates Shifts in Soil N2/N2O Ratios

The increase in atmospheric nitrous oxide (N₂O), a potent greenhouse and ozone depleting gas, is of serious global concern. Soils are large contributors to this increase through microbial processes that are enhanced in agricultural land due to nitrogenous fertilizer applications. Denitrification, a respiratory process using nitrogen oxides as electron acceptors in the absence of oxygen, is the main source of N₂O. The end product of denitrification is benign dinitrogen (N₂) and understanding what regulates the shift in ratio of N₂O and N₂ emission is crucial for mitigation strategies. The role of organic carbon in controlling N₂O reduction is poorly understood, and mostly based on application of glucose. Here we investigated how a range of carbon compounds (succinate, butyrate, malic acid, acetate, glucose, sucrose and cysteine) affect denitrifier N₂/N₂O production stoichiometry under laboratory conditions. The results show that a soil''s capability in efficiently reducing N₂O to N₂ is C substrate dependent and most compounds tested were different in regards to this efficiency compared to glucose. We challenge the concept of using glucose as a model soil C compound in furthering our understanding of denitrification and specifically the efficiency in the N₂O reductase enzyme. Organic acids, commonly exuded by roots, increased N₂/N₂O ratios compared to glucose, and therefore mitigated net N₂O release and we suggest provides better insights into soil regulatory aspects of N₂O reduction. The widespread use of glucose in soil laboratory studies could lead to misleading knowledge on the functioning of denitrification in soils with regards to N₂O reduction.     

Plant Functional Diversity and Species Diversity in the Mongolian Steppe

Background

The Mongolian steppe is one of the most important grasslands in the world but suffers from aridization and damage from anthropogenic activities. Understanding structure and function of this community is important for the ecological conservation, but has seldom been investigated.

Methodology/Principal Findings

In this study, a total of 324 quadrats located on the three main types of Mongolian steppes were surveyed. Early-season perennial forbs (37% of total importance value), late-season annual forbs (33%) and late-season perennial forbs (44%) were dominant in meadow, typical and desert steppes, respectively. Species richness, diversity and plant functional type (PFT) richness decreased from the meadow, via typical to desert steppes, but evenness increased; PFT diversity in the desert and meadow steppes was higher than that in typical steppe. However, above-ground net primary productivity (ANPP) was far lower in desert steppe than in the other two steppes. In addition, the slope of the relationship between species richness and PFT richness increased from the meadow, via typical to desert steppes. Similarly, with an increase in species diversity, PFT diversity increased more quickly in both the desert and typical steppes than that in meadow steppe. Random resampling suggested that this coordination was partly due to a sampling effect of diversity.

Conclusions/Significance

These results indicate that desert steppe should be strictly protected because of its limited functional redundancy, which its ecological functioning is sensitive to species loss. In contrast, despite high potential forage production shared by the meadow and typical steppes, management of these two types of steppes should be different: meadow steppe should be preserved due to its higher conservation value characterized by more species redundancy and higher spatial heterogeneity, while typical steppe could be utilized moderately because its dominant grass genus Stipa is resistant to herbivory and drought.     

Variability in Bioreactivity Linked to Changes in Size and Zeta Potential of Diesel Exhaust Particles in Human Immune Cells

Acting as fuel combustion catalysts to increase fuel economy, cerium dioxide (ceria, CeO₂) nanoparticles have been used in Europe as diesel fuel additives (Envirox™). We attempted to examine the effects of particles emitted from a diesel engine burning either diesel (diesel exhaust particles, DEP) or diesel doped with various concentrations of CeO₂ (DEP-Env) on innate immune responses in THP-1 and primary human peripheral blood mononuclear cells (PBMC). Batches of DEP and DEP-Env were obtained on three separate occasions using identical collection and extraction protocols with the aim of determining the reproducibility of particles generated at different times. However, we observed significant differences in size and surface charge (zeta potential) of the DEP and DEP-Env across the three batches. We also observed that exposure of THP-1 cells and PBMC to identical concentrations of DEP and DEP-Env from the three batches resulted in statistically significant differences in bioreactivity as determined by IL-1β, TNF-α, IL-6, IFN-γ, and IL-12p40 mRNA (by qRT-PCR) and protein expression (by ELISPOT assays). Importantly, bioreactivity was noted in very tight ranges of DEP size (60 to 120 nm) and zeta potential (−37 to −41 mV). Thus, these physical properties of DEP and DEP-Env were found to be the primary determinants of the bioreactivity measured in this study. Our findings also point to the potential risk of over- or under- estimation of expected bioreactivity effects (and by inference of public health risks) from bulk DEP use without taking into account potential batch-to-batch variations in physical (and possibly chemical) properties.     

Changes in Bacterial and Archaeal Community Structure and Functional Diversity along a Geochemically Variable Soil Profile

Spatial heterogeneity in physical, chemical, and biological properties of soils allows for the proliferation of diverse microbial communities. Factors influencing the structuring of microbial communities, including availability of nutrients and water, pH, and soil texture, can vary considerably with soil depth and within soil aggregates. Here we investigated changes in the microbial and functional communities within soil aggregates obtained along a soil profile spanning the surface, vadose zone, and saturated soil environments. The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes (amoA and dsrAB) as well as cultivation-based analysis of Fe(III)-reducing organisms. Here we found that the microbial communities and putative ammonia-oxidizing and Fe(III)-reducing communities varied greatly along the soil profile, likely reflecting differences in carbon availability, water content, and pH. In particular, the Crenarchaeota 16S rRNA sequences are largely unique to each horizon, sharing a distribution and diversity similar to those of the putative (amoA-based) ammonia-oxidizing archaeal community. Anaerobic microenvironments within soil aggregates also appear to allow for both anaerobic- and aerobic-based metabolisms, further highlighting the complexity and spatial heterogeneity impacting microbial community structure and metabolic potential within soils.     

Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Changes in Marsh Elevation,Edaphic Conditions and Plant Host Species

An important source of new nitrogen in salt marsh ecosystems is microbial diazotrophy (nitrogen fixation). The diazotroph assemblages associated with the rhizospheres (sediment directly affected by the roots) of salt marsh plants are highly diverse, somewhat stable, and consist mainly of novel organisms. In Crab Haul Creek Basin, North Inlet, SC, the distribution of plant types into discrete zones is dictated by relatively minor differences in marsh elevation and it was hypothesized that the biotic and abiotic properties of the plant zones would also dictate the composition of the rhizosphere diazotroph assemblages. Over a period of 1 year, rhizosphere sediments were collected from monotypic stands of the black needlerush, Juncus roemerianus, the common pickleweed, Salicornia virginica, the short and tall growth forms of the smooth cordgrass Spartina alterniflora, and a mixed zone of co-occurring S. virginica and short form, S. alterniflora. DNA was extracted, purified and nifH sequences PCR amplified for denaturing gradient gel electrophoresis (DGGE) analysis to determine the composition of the diazotroph assemblages. The diazotroph assemblages were strongly influenced by season, abiotic environmental parameters and plant host. Sediment chemistry and nitrogen fixation activity were also significantly influenced by seasonal changes. DGGE bands that significantly affected seasonal and zone specific clustering were identified and most of these sequences were from novel diazotrophs, unaffiliated with any previously described organisms. At least one third of the recovered nifH sequences were from a diverse assemblage of Chlorobia, and γ-, α-, β- and δ-Proteobacteria. Diazotrophs that occurred throughout the growing season and among all zones (frequently detected) were also mostly novel. These significant sequences indicated that diazotrophs driving the structure of the assemblages were diverse, versatile, and some were ubiquitous while others were seasonally responsive. Several ubiquitous sequences were closely related to sequences of actively N₂ fixing diazotrophs previously recovered from this system. These sequences from ubiquitous and versatile organisms likely indicate the diazotrophs in these rhizosphere assemblages that significantly contribute to ecosystem function.     

Contrasting Patterns of Soil Chemistry and Vegetation Cover Determine Diversity Changes of Soil Phototrophs Along an Afrotropical Elevation Gradient

Ecosystems - Soil phototrophic microbes play key roles in many ecosystem functions, including nutrient cycling, water absorption and retention, substrate weathering and soil stabilization, as well...     

Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment

The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR), a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR) and C. floccosa-transformed DOR (CORDOR) on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR.