Effects of biological soil crusts on soil nematode communities following dune stabilization in the Tengger Desert,Northern China

Biological soil crusts (BSCs) play an important role in the dune fixation and maintaining soil biota in arid desert systems. Free-living soil nematode communities could be used as significant bioindicators to reflect soil recover regime after sand burial. However, the relationship between BSCs and nematodes is rarely known. To examine the effects of BSCs on soil nematodes, 72 soil samples under cyanobacteria–lichen and moss crusts were collected to analyse nematode communities in the different aged vegetated areas at the southeastern edge of the Tengger Desert. Our results showed the colonization and development of BSCs significantly enhanced nematode diversity. Nematode abundances, generic richness, H′, MI, EI and SI were greater under crusts than those under noncrust. In particular, nematode abundances, generic richness, H′, MI, EI and SI were positively correlated with crust ages. The differences in nematode communities were also dependent upon crust types. Nematode abundances and generic richness under moss crusts were higher than those under cyanobacteria–lichen crusts. This can be contributed to the present and succession of BSCs that increased thickness of topsoil after dunes have been stabilized, namely, creating suitable habitats and providing an essential food source for nematodes.     

Plant monocultures produce more antagonistic soil Streptomyces communities than high-diversity plant communities

Plant–soil feedbacks are important to productivity and plant community dynamics in both natural and managed ecosystems. Among soil bacteria, the Streptomyces possess particularly strong antagonistic activities and inhibit diverse plant pathogens, offering a clear pathway to involvement in plant–soil feedbacks. We hypothesized that feedback effects and the ability of individual host plant species to foster antagonistic Streptomyces populations may be modified by the richness of the surrounding plant community. To test this, we collected soil associated with four different plant species (two C4 grasses: Andropogon gerardii, Schizachyrium scoparium; and two legumes: Lespedeza capitata, Lupinus perennis), grown in communities that spanned a gradient of plant species richness (1, 4, 8, 16, or 32 species). For each of these soils, we characterized the potential of soil Streptomyces to antagonize plant pathogens, using an in vitro plate assay with indicator strains to reveal inhibition. We cultivated each plant species in each conditioned soil to assess feedback effects on subsequent plant growth performance. Surrounding plant richness modified the impacts of particular plant species on Streptomyces antagonistic activity; A. gerardii supported a higher proportion of antagonistic Streptomyces when grown in monoculture than when grown in 32-spp plant communities, and L. capitata supported more strongly antagonistic Streptomyces when grown in 4- or 32-spp plant communities than in 8-spp plant communities. Similarly, the feedback effects of particular plant species sometimes varied with surrounding plant richness; aboveground biomass production varied with plant species richness for A. gerardii in L. perennis-trained soil, for L. capitata in A. gerardii-trained soil, and for L. perennis in L. capitata-trained soil. Streptomyces antagonist density increased with overall Streptomyces density under low but not under high plant richness, suggesting that plant diversity modifies selection for antagonistic phenotypes among soil Streptomyces. This work highlights the complexity of feedback dynamics among plant species, and of plant–microbiome interactions in soil.     

中国腾格里沙漠生物土壤结皮中的可培养微真菌群落

Biological soil crusts are essential components of arid ecosystems. We examined the variations in microfungal communities inhabiting different biological crust types in the vicinity of the Shapotou Research Station in the Tengger Desert, China. A total of 134 species from 66 genera were isolated using the soil dilution plate method. The mycobiota of the crusts from the Tengger Desert, similar to that of the Negev Desert in Israel, was dominated by melanin-containing species with large multicellular spores. Abundance of these xeric species increased spatially with increasing xeric conditions from moss-dominated to cyanobacterial crusts. Density of microfungal isolates displayed the opposite trend and was positively correlated with chlorophyll content, indicating the possible significant influence of organic matter content and wetness duration on fungal biomass. Within a chronosequence of the localities of different periods after sand stabilization with revegetation, little variations were revealed in species composition and isolate density of the crust microfungal communities, while a tendency towards a decrease in the community diversity level with the crust age was noted. Microfungal communities from stabilized localities differed from those of the natural localities in abundance of the dominant and some frequent species, and in the fluctuations of diversity characteristics between the cyanobacterial and moss-dominated crusts. The variations in mycobiotic parameters in the soil crusts of the Tengger Desert were apparently associated with the topographically induced variations in abiotic conditions, while the differences in microfungal community of soil crusts between the Tengger and Negev deserts, such as the significantly higher abundance of thermotolerant species in the crusts of the Tengger Deserts, were caused by the principal differences in their precipitation regimes, associated with different rainy seasons, winter and summer in the Negev and Tengger deserts, respectively.     

Alphaproteobacteria communities depend more on soil types than land managements

Soil properties and agricultural practices take a joint effect on the communities of soil bacteria. The aim of the present study was to survey Alphaproteobacterial communities as possible indicators of soil quality considering clay, loamy and sandy soils under conventional and organic farming. Alphaproteobacteria community composition were analysed by 16S rRNA gene with nested-PCR (polymerase chain reaction) and denaturing gradient gelelectrophoresis (DGGE). Sequencing of partial 16S rRNA gene from the DGGE bands were performed. Conventional and organic farming resulted in significant differences in chemical properties of soils. According to the results community fingerprints were separated into groups depending on soil types and farming systems. This separation can be attributed mostly to soil pH, AL-P₂O₅,-K₂O. The analysed sequences were identified as soil bacteria which could play the main role in nitrogen fixing, mineralisation and denitrification. The highest diversity index was revealed from the organic farming at sandy texture site, where mainly Mesorhizobium sp. and Rhizobium sp. were detected. The soil type and actual crop could have a stronger impact on the soil bacterial composition than the management.     

Bacterial communities are more dependent on soil type than fertilizer type, but the reverse is true for fungal communities

The soil microbial community is strongly influenced by a wide variety of factors, such as soil characteristics and field management systems. In order to use biological indicators based on microbial community structure, it is very important to know whether or not these factors can be controlled. The present study aimed to determine whether soil type or fertilization has a greater influence on the soil microbial community based on denaturing gradient gel electrophoresis (DGGE) analysis of 12 experimental field plots containing four different soil types, Cumulic Andosol, Low-humic Andosol, Yellow Soil and Gray Lowland Soil, kept under three different fertilizer management systems since 2001 (the application of chemical fertilizer, the application of rice husk and cow manure, and the application of pig manure). Bacterial DGGE analysis using 16S rRNA genes and fungal DGGE analysis using 18S rRNA genes revealed that the bacterial community was related to the soil type more than the fertilization; however, the fungal community was related to the fertilization more than the soil type. These results might suggest that the fungal community is easier to control by fertilization than the bacterial community. Thus, we propose that indicators based on the fungal community might be more suitable as microbial indicators for soil quality.     

Spatial distribution and physiology of biological soil crusts from semi-arid central Spain are related to soil chemistry and shrub cover

Despite the critical role of biological soil crusts (BSCs) in arid and semi-arid ecosystem function, few studies are found concerning the most important environmental variables affecting their distribution and physiology. This study seeks to determine soil and microenvironmental factors affecting the spatial distribution and pigment production of BSC-forming lichens and mosses in open patches of a semi-arid Mediterranean kermes oak thicket. We measured late-successional BSC cover, shrub cover, distance to nearest kermes oak (to test for effects of kermes oak thicket microenvironment on BSC), and pigment concentration of one lichen (Cladonia foliacea) and one moss (Pleurochaete squarrosa) species in the Nature Reserve El Regajal-Mar de Ontígola (Central Spain). At the macroscale (>0.5 m), results showed that BSC distribution and pigments were tightly coupled to a suite of soil properties, in particular soil pH, Fe, and Ca. Specifically, soil pH had a positive relationship with the cover of five individual BSC-forming lichen species and was negatively related to pigment production in C. foliacea. When pH was excluded from the analysis, Ca appeared as the main soil variable and was correlated with total BSC cover and total lichen cover. The micronutrient Fe had a significant positive relationship with the concentration of eight pigments in P. squarrosa and was also coupled with the cover of two BSC-forming lichens. Manganese, previously proposed as a key limiting micronutrient for BSCs, affected lichen diversity in a negative way. At the microscale (∼0.5 m), kermes oak microenvironment, shrub cover, and moss cover were determinants of BSC distribution, and total lichen and total BSC cover were overrepresented on N and E-facing shrub microsites. Our findings suggest that soil chemical variability and microsite diversity created by neighbouring vegetation affect BSC distribution in complex and essential ways and that studies aiming to explore BSC-environment relationships should be conducted at various spatial scales. Studies based on species- or group-specific responses are, thus, inadequate to unveil the main factors determining the distribution of the diverse organisms that constitute BSCs and/or to propose potential tools aiming to restore BSC in arid and semiarid ecosystems.     

Biodiversity and trophic structure of soil nematode communities are altered following woody plant invasion of grassland

Woody plant encroachment is an important land cover change in dryland ecosystems throughout the world, and frequently alters above and belowground primary productivity, hydrology, and soil microbial biomass and activity. However, there is little known regarding the impact of this geographically widespread vegetation change on the biodiversity and trophic structure of soil fauna. Nematodes represent a major component of the soil microfauna whose community composition and trophic structure could be strongly influenced by the changes in ecosystem structure and function that accompany woody encroachment. Our purpose was to characterize nematode community composition and trophic structure along a grassland to woodland chronosequence in the Rio Grande Plains of southern Texas. Research was conducted at the La Copita Research Area where woody encroachment has been documented previously. Soil cores (0–10 cm) were collected in fall 2006 and spring 2007 from remnant grasslands and woody plant stands ranging in age from 15 to 86 years, and nematodes were extracted by sugar centrifugation. Neither nematode densities (3200–13,800 individuals kg⁻¹ soil) nor family richness (15–19 families 100 g⁻¹ soil) were altered by woody encroachment. However, family evenness decreased dramatically in woody stands >30 years old. This change in evenness corresponded to modifications in the trophic structure of nematode communities following grassland to woodland conversion. Although root biomass was 2–5× greater in wooded areas, root-parasitic nematodes decreased from 40% of all nematodes in grasslands to <10% in the older wooded areas, suggesting the quality (C:N or biochemical defenses) of woody plant root tissue could be limiting root-parasites. In contrast, bacterivores increased from 30% of nematodes in grasslands to 70–80% in older woody patches. This large increase in bacterivores may be a response to the 1.5–2.5× increase in soil microbial biomass (bacteria + fungi) following woody encroachment. Therefore, while energy flow through grassland nematode communities appears to be distributed nearly equally among herbivory, fungivory and bacterivory, the energy flow through nematode communities in wooded areas appears to be based primarily on bacterivory. We speculate that these shifts in nematode community composition and trophic structure could have important implications for ecosystem patterns and processes. First, the low abundance of root-parasitic nematodes (and presumably root herbivory) under woody plants may be one mechanism by which woody plants are able to establish and compete effectively with grasses during succession from grassland to woodland. Second, the large increase in bacterivores following woody encroachment likely accelerates microbial turnover and the mineralization of N, thereby providing a feedback that enables the persistence of N-rich woody plant communities.     

Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils

Soil microbial communities in dryland ecosystems play important roles as root associates of the widely spaced plants and as the dominant members of biological soil crusts (biocrusts) colonizing the plant interspaces. We employed rRNA gene sequencing (bacterial 16S/fungal large subunit) and shotgun metagenomic sequencing to compare the microbial communities inhabiting the root zones of the dominant shrub, Larrea tridentata (creosote bush), and the interspace biocrusts in a Mojave desert shrubland within the Nevada Free Air CO₂ Enrichment (FACE) experiment. Most of the numerically abundant bacteria and fungi were present in both the biocrusts and root zones, although the proportional abundance of those members differed significantly between habitats. Biocrust bacteria were predominantly Cyanobacteria while root zones harbored significantly more Actinobacteria and Proteobacteria. Pezizomycetes fungi dominated the biocrusts while Dothideomycetes were highest in root zones. Functional gene abundances in metagenome sequence datasets reflected the taxonomic differences noted in the 16S rRNA datasets. For example, functional categories related to photosynthesis, circadian clock proteins, and heterocyst-associated genes were enriched in the biocrusts, where populations of Cyanobacteria were larger. Genes related to potassium metabolism were also more abundant in the biocrusts, suggesting differences in nutrient cycling between biocrusts and root zones. Finally, ten years of elevated atmospheric CO₂ did not result in large shifts in taxonomic composition of the bacterial or fungal communities or the functional gene inventories in the shotgun metagenomes.     

Plant roots are more important than temperature in modulating carbon release in a limed acidic soil

Lime is a common amendment to overcome soil acidity in agricultural production systems. However, plant root effects on lime and soil carbon (C) dynamics in acidic soils under varied temperature remain largely unknown. We monitored root effects of soybean on the fate of lime applied to an acidic soil at 20 and 30°C in growth chambers. Soil respired CO₂ was continuously trapped in columns without and with plants until the final stage of vegetative growth. Lime‐derived CO₂ was separated from total respired CO₂ based on δ¹³C measurements in CO₂. Leaching was induced at early and late vegetative growth stages, and the leachates were analysed for dissolved organic (DOC) and inorganic C (DIC) concentrations. Soil respiration significantly increased with lime addition at both temperatures (p < 0.001). The presence of soybean doubled the recovery of lime‐derived CO₂‐C at 20°C at the early growth stage; however, by the end of the experiment, the contribution of lime‐derived CO₂‐C to soil respiration was negligible in all treatments, indicating that the contribution of lime to soil respiration was shortlived. In contrast, DIC and DOC concentrations in leachates remained elevated with liming and were greater in the presence of soybean. We observed no main temperature effects and no interactive effects of temperature and soybean presence on lime‐derived CO₂‐C, DIC and DOC. These results highlight the role of plant‐modulated processes in CO₂ release and C leaching from lime in acidic soils, whereas an increase in temperature may be less important. Temperature and plant roots alter the rate of key processes controlling C dynamics in a limed acidic soil. Lime‐derived CO₂‐C, DIC and DOC increased more in the presence of plants than with increased temperature. Root effects are more important than temperature for inorganic and organic carbon dynamics in limed acidic soils.     

Soil amendment with city sewage sludge increases soil extractable cadmium,nickel and zinc more than tannery,pharmaceutical and paper mill wastes

Abstract

The distribution of DTPA-extractable Cd, Ni and Zn in four profile samples collected from areas contaminated with wastes from tannery, city sewage, pharmaceutical and paper mills located at different places in Bangladesh was investigated. Soil samples were analysed for the total and their DTPA-extractable metal contents. The total concentration of metals in the soil horizons ranged from 0.07 to 0.62 mg kg^?1 for Cd, 31 to 54 mg kg^?1 for Ni and 59 to 838 mg kg^?1 for Zn, respectively. These metal concentrations were highest in the surface and lowest in the subsurface horizons. This trend was also observed for the DTPA-extractable amounts of these metals. The relative extractability, expressed as the ratio of DTPA to total contents (aqua regia-extractable) was 33 to 46% for Cd, 2 to 10% for Ni and 3 to 28% for Zn, respectively, in the A1 horizon, while in the B and C horizons the ratios decreased gradually as did total concentration, indicating that metal contamination was primarily limited to the surface horizon. For all three metals, the above mentioned ratio was highest in the city sewage soil and the lowest in the paper mill soil. In general, the extent of contamination among the profiles investigated was in the following order: city sewage>tannery>pharmaceutical>paper mill soil. Higher ratios of DTPA-extractable Cd, Ni and Zn in the city sewage soil than the other soils may create a risk for the contamination of agricultural products and ground water.