Soil Assemblages Research Articles

Differential degradation of polycyclic aromatic hydrocarbon mixtures by indigenous microbial assemblages in soil.

Environmental contamination by polycyclic aromatic hydrocarbons (PAHs) typically occurs as mixtures of compounds. In this study, the response of indigenous soil bacterial and fungal communities to mixtures containing phenanthrene, fluoranthene and benzo(a)pyrene in various combinations was examined using molecular fingerprinting techniques and quantification of a key PAH degradative gene. Results were compared to a parallel study by Sawulski etal. (2014) which examined the effect of these PAHs on soil microbial communities when added as single contaminants. The rate of degradation of individual PAHs varied depending on whether the PAH was present as a single contaminant or in a mixture; phenanthrene was degraded most rapidly when present as a sole contaminant, fluoranthene was removed faster in the presence of the lower molecular weight phenanthrene and the rate of benzo(a)pyrene degradation was reduced in the presence of the 4-ring PAH, fluoranthene. Bacterial and fungal assemblages differed significantly between treatments regardless of which PAH was added to soil. Although less abundant than the Gram-negative PAH-RHDα gene, the gene associated with Gram-positive bacteria responded to a greater extent to the presence of PAHs, either as single compounds or as mixtures and this increase was significantly correlated with PAH degradation. Contaminated sites generally contain complex mixtures of pollutants. Development of effective bioremediation strategies for contaminated soils requires knowledge of the response of soil microbial communities to such mixtures. This study provides information on the degradation of different mixtures of three priority pollutants in soil with a history of polycyclic aromatic hydrocarbon contamination and examines the response of soil bacterial and fungal communities to the presence of these pollutants as sole contaminants or as part of a mixture. This is one of few studies to-date to compare the effects of single compounds and pollutant mixtures on more than one soil microbial community.

Soil nematode assemblages in an acid soil as affected by lime application

Liming can affect soil biota through alterations in soil pH and soil structure. Many earlier studies monitored the responses of soil nematode communities to lime application but they did not come to a consensus and did not use indices of soil nematode community and multivariate statistical approaches developed over the past two decades. The present research explored the short-term effects of lime application on soil nematode communities in an acrisol in threeEucalyptusplantations in southern China. Nematodes were sampled from control and lime-treated plots at three periods from October 2011 to February 2012 at 0-10 cm and 10-20 cm soil depths. Repeated measures ANOVA showed that lime application significantly reduced the abundance of herbivores at 10-20 cm depth during the study. Lime application tended to increase the bacterivore index at 0-10 cm depth over time. Principal response curves of soil nematode community structure, in terms of nematode trophic group composition, revealed that the differences between control and lime application treatments increased over time, primarily because of the decline of fungivores in plots treated with lime. The decline in fungivores resulted mainly from declines ofFilenchusandDitylenchus. The results suggest that the fungal-mediated decomposition channel in the soil food web was suppressed by lime application. Our study also demonstrated that the sensitivity of different nematode genera to lime application varied widely, even for genera within the same trophic group. In particular, the abundance of several bacterivorous genera (Prismatolaimus,Plectus,Wilsonema,Protorhabditis,DiploscapterandHeterocephalobus) gradually declined and that ofRhabditonemaat 0-10 cm depth gradually increased following lime application during the study; two herbivorous genera,TrophotylenchulusandHelicotylenchus, had opposite responses to lime application at 0-10 cm depth. Integrating univariate statistical approaches with multivariate approaches facilitated the analysis of soil nematode responses to lime application.

Influence of the local environment on lacustrine sedimentary phytolith records

Fossil phytolith assemblages from soils and lake sediments are widely used to reconstruct past vegetation patterns and dynamics, especially in tropical environments where a phytolith index has been quantitatively calibrated to estimate tree cover. Most calibration studies have focused on comparing phytolith assemblages in modern soil with the present aboveground vegetation. However, little is known about phytolith taphonomy and the representativeness of phytolith assemblages and indices in lake sediments. The aim of this study is to improve the understanding of the composition of phytolith assemblages and their influx into recent lake sediments by comparing them with local land cover assessments. This study focused on three lakes in the Central African Republic located in savanna, forest–savanna mosaic, and forest. It appears that the local environment surrounding the lake was critical for interpreting current and past assemblages, and the ratio of dicotyledon to Poaceae diagnostic phytoliths (the D/P index). The presence of a riparian forest in an open environment had no impact on phytolith assemblages or the D/P index, which instead reflected both the local and regional landscapes. Conversely, contributions from a marsh, if present in a forested environment, completely dominated the phytolith records, which consequently reflected only the local environment of the lake. A high correlation between the Poaceae phytoliths influxes and the charcoal accumulation rates for the two lakes surrounded by a riparian forest has also been found. This finding, which was associated with a high proportion of burned Poaceae phytoliths, provides evidence that Poaceae phytoliths are mainly transported by wind in ash clouds produced by fires.

Diversified diazotrophs associated with the rhizosphere of Western Indian Himalayan native red kidney beans (Phaseolus vulgaris L.).

Red kidney beans (RKBs) are one of the major components in the human diet of Western Indian Himalaya (WIH). Their cultivation in these habitats is strongly influenced by various biotic and abiotic stresses and therefore, there must be a selection of RKB associated microorganisms that are adapted to these harsh conditions. Seven cold adaptive diazotrophs from the same rhizosphere were isolated in our previous study to reveal the low-temperature associated proteins and mechanisms. However, the diversity and phylogenetic affiliations of these rhizosphere diazotrophs are still unknown. In this study, RKB rhizospheric soil from two different agro-ecosystems of WIH namely S1 (Chhiplakot, 30.70°N/80.30°E) and S2 (Munsyari, 30.60°N/80.20°E) were explored for the assessment of nitrogenase reductase gene (nifH) diversity by plating respective clone libraries SN1 and SN2. The RKB rhizosphere diazotroph assemblage was very diverse and apparently consists mainly of the genera Rhizobium, followed by unknown diazotrophic microorganisms. Deduced amino acid sequence analysis revealed the presence of diverse nifH sequences, affiliated with a wide range of taxa, encompassing members of the Proteobacteria, Actinobacteria and Firmicutes. Members of cyanobacteria, methanotrophs and archaea were also detected. To the best of our knowledge, this is the first major metagenomic effort that revealed the presence of diverse nitrogen-fixing microbial assemblages in indigenous RKB rhizospheric soil which can further be explored for improved crop yield/productivity.Electronic supplementary materialThe online version of this article (doi:10.1007/s13205-014-0238-5) contains supplementary material, which is available to authorized users.

Predominant bacterial and fungal assemblages in agricultural soils during a record drought/heat wave and linkages to enzyme activities of biogeochemical cycling

Identification of microbial assemblages predominant under natural extreme climatic events will aid in our understanding of the resilience and resistance of microbial communities to climate change. From November 2010 to August 2011, the Southern High Plains (SHP) of Texas, USA, received only 39.6mm of precipitation (vs. the historical average of 373mm) and experienced the three hottest months (June–August 2011) since record keeping began in 1911. The objective of this study was to characterize soil bacterial (16 S rRNA gene) and fungal (internal transcribed spacer 1–4, ITS1-ITS4) species distribution and diversity via pyrosequencing during the peak of the drought/heat wave in July 2011 and when the Drought Index and temperatures were lower in March 2012. Samples were collected from two different soil types (loam and sandy loam) under two different dryland cropping histories (monoculture vs. rotation). Fungal Diversity Indexes were significantly higher after the drought/heat wave while Bacterial Indexes were similar. Bacterial phyla distribution in July 2011 was characterized by lower relative abundance of Acidobacteriaand Verrucomicrobia, and greater relative abundance of Proteobacteria, Chloroflexi, Actinobacteria and Nitrospirae than March 2012 samples. Further grouping of pyrosequencing data revealed approximately equal relative proportions of Gram positive (G+) and Gram negative (G−) bacteria in July 2011, while G− bacteria predominated in March 2012. Fungal class Dothideomycetes was approximately two times greater in July 2011 than in March 2012, while the class Sordariomycetes and a group of unidentified OTUs from Ascomycota increased from July 2011 to March 2012. Microbial community composition was less influenced by management history than by the difference in climatic conditions between the sampling times. Correspondence analysis identified assemblages of fungal and bacterial taxa associated with greater enzyme activities (EAs) of C, N, or P cycling found during the drought/heat wave. Microbial assemblages associated with arylsulfatase activity (key to S cycling), which increased after the drought/heat wave, were identified (Streptomyces parvisporogenes, Terrimonas ferruginea and Syntrophobacter sp.) regardless of the soil and management history. The distinct microbial composition found in July 2011 may represent assemblages essential to maintaining ecosystem function during extreme drought and intense heat waves in semiarid agroecosystems.

Relationships between nematode diversity, plant biomass, nutrient cycling and soil suppressiveness in fumigated soils

Nematodes interact with many other organisms as participants in several links of the soil food web, playing important roles in essential soil processes. Due to their high abundance and diversity of responses to soil disturbance, nematodes are suitable indicators of soil condition. With the aim of inferring soil fumigation effects on agroecosystem functioning, soil nematode diversity, soil properties, plant growth, and soil suppressiveness were monitored in a commercial strawberry farm and its surroundings for two consecutive growing seasons in southern Spain. Our results show that nematode diversity was low in fumigated soils throughout the whole season and, although yearly recovery occurred within the treated fields, fumigated soils showed a permanent perturbed condition. The nematode community was more closely associated to nutrient cycling in non-cropped than in cropped soils, and the link between plant biomass and nematode community structure was weak. Non-treated furrows within the treated fields were a reservoir of both beneficial and plant-parasitic nematodes, but such difference between furrows and beds was not enough to maintain more suppressive soil assemblages in the furrows. Treated soils were less suppressive than unmanaged soils, and there was a positive and significant correlation between soil suppressiveness and soil food web structure and diversity.

Hydraulic and Physiochemical Properties of a Hillslope Soil Assemblage in the Ozark Highlands

Heterogeneity of infiltration and subsurface redistribution of soil water can have a profound influence on plant growth and productivity as well as water quality. However, substantial uncertainty exists in assessing hydrologic impacts over multiple scales confounded by multiple adjacent land uses. Spatial variabilities of soil surface hydraulic properties are key elements in understanding vadose zone hydrodynamics. The objective of this investigation was to evaluate the effects of land use, soil series, and microtopographic position on soil surface physiochemical and hydraulic properties (i.e., ponded and tension infiltration) during the transition from fall to winter seasons during a period of shallow aquifer recharge. Measurements were made across three Fragiudults (Captina, Nixa, and Johnsburg soil series) on a young alley-cropped agroforestry tract and an adjacent cattle-grazed pasture that constitute a headwater hillslope soil assemblage in the Ozark Highlands. Ponded and tension infiltration rates were affected (P < 0.05) by soils, microtopographic positions, and/or land uses. Tension infiltration rates, averaged across soils and land uses at a pressure head of -3 cm, were nearly twofold greater at the microtopographic low position (17.8 mm h−1) than the high (9.2 mm h−1) position, where the microtopographic high position in the landscape was generally a shallower soil than that at the microtopographic low position. However, when all infiltration measurements were evaluated together, no significant differences in infiltration dynamics were observed among soils, microtopographic positions, or land uses. Thus, a single infiltration pressure head function effectively characterized the hillslope soil assemblage evaluated in this study when shallow aquifer recharge was occurring. Greater bioporosity in upland grazed pastures may serve to naturally decrease hydraulic property variability across soils, which may simplify, rather than complicate, hydrologic partitioning between infiltration and runoff in grassland-based agroecosystems receiving frequent applications of animal manures in the Ozark Highlands.

Arsenic (As), antimony (Sb), and lead (Pb) availability from Au-mine Technosols: a case study of transfer to natural vegetation cover in temperate climates

Soils from old Au-mine tailings (La Petite Faye, France) were investigated in relation to the natural vegetation cover to evaluate the risk of metals and metalloids (Pb, As, Sb) mobilizing and their potential transfer to native plants (Graminea, Betula pendula, Pteridium aquilinum, Equisetum telmateia). The soils are classified as Technosols with high contamination levels of As, Pb, and Sb. The single selective extractions tested to evaluate available fraction (CaCl2, acetic acid, A-Rhizo, and DTPA) showed low labile fractions (<5 % of bulk soil contents), but still significant levels were observed (up to 342.6 and 391.9 mg/kg for As and Pb, respectively) due to the high contamination levels of soils. Even at high soil contaminations (considered as phytotoxic levels for plants), translocation factors for native plants studied are very low resulting in low concentrations of As, Sb, and Pb in their aerial part tissues. This study demonstrates the important role of (1) native plant cover in terms of "stabilization" of these contaminants, and (2) the poor effectiveness of extraction procedures used for this type of soil assemblages, i.e., rich in specific mineral phases.

Phytoliths of Southeastern Vancouver Island, Canada, and their potential use to reconstruct shifting boundaries between Douglas-fir forest and oak savannah

Phytolith assemblages in terrestrial soils have the potential to reveal local shifts between open savannah and conifer forests in the past. On southeastern Vancouver Island, this could help quantify the range of variability of Garry oak savannahs prior to European colonization, and the degree of influence of indigenous people in maintaining open savannahs. We catalogued the phytolith morphotypes found in 72 of the most common plant species in this system, and extracted phytoliths from two soil cores on either side of the boundary between a conifer forest and an oak savannah. Grasses are the most prolific producers of phytoliths in savannahs. In forests, Douglas-fir (Pseudotsuga menziesii) produces large, distinctive asterosclereid phytoliths. Phytolith assemblages from soil cores showed that phytoliths from grasses dominated, even in soils from the forest, where grasses are rare. However, the presence of asterosclereid phytoliths reliably distinguished between Douglas-fir forest and Garry oak savannah habitats within 20m of the vegetation boundary. This finding may be useful for reconstructing past vegetation not only on Vancouver Island, but also across a large geographic area in North America where grasslands tend to be invaded by Douglas-fir following fire suppression. The use of the phytolith record from terrestrial soils at local sites where the history of human occupation is well-known could help establish the degree of influence of indigenous peoples in maintaining open savannahs on southeastern Vancouver Island.

Representational bias in phytoliths from modern soils of central North America: Implications for paleovegetation reconstructions

Understanding localized patterns and community compositions of vegetation in an environment is critical to the reconstruction of climatic and ecological conditions across all spatiotemporal scales. One of the most accurate and useful ways to characterize vegetation, and therefore to describe the climatic and ecological conditions of a location, is through the plant fossil record. Phytoliths (plant silica microfossils) are often preserved in the absence of other paleobotanical data and are becoming more widely used for deep-time vegetation reconstructions. Significant work has been done to standardize the analytical methodology of phytolith extraction, statistical analysis, and interpretation, but more detailed investigations are needed to understand how well a given soil assemblage represents the actual aboveground plant biomass for a given ecosystem.We present results from paired soil phytolith assemblages and local vegetation assemblages across the central United States, including temperate forest, grassland, and rangeland/scrubland ecosystems. Phytolith assemblages obtained via extractions from soil A-horizons were compared to percent cover of species and plant biomass estimates obtained via in situ field observations and aerial estimates of tree cover to analyze differences in the relative abundance of forest/woody vegetation vs. grasses. Soil phytolith assemblages from all sites average a 29% bias toward the grass morphotypes as compared to actual aboveground biomass observations, and comparisons to percent cover yielded broadly comparable bias figures. Percent bias estimates do not show significant correlations to most environmental factors (temperature, precipitation, local elevation), however, an extremely strong correlation (p<0.001) was observed with soil order type. This is likely due to the fact that soil order reflects both vegetation type and chemical factors known to affect overall phytolith assemblages; therefore, soil order is a proxy that aggregates several sources of bias. As a result, we suggest further research into the development of correction factors between phytolith sample assemblages and their interpreted past counterpart ecosystems based on estimates derived from modern analyses of each major soil order type. Such background corrections are essential to the continued use of phytoliths as a proxy for past vegetation and ecological reconstructions of temperate ecosystems throughout the Phanerozoic record.

Soil geography and diversity of the European biogeographical regions

For decades, soil geography has been mainly a qualitative and descriptive discipline. There are now technologies and mathematical tools available that allow formalizing soil geography in more quantitative terms. In this paper, the distribution and diversity of the soils of Europe are analyzed using GIS tools and pedodiversity algorithms. Soil data were taken from the European Soil Database (V2.0) and computed within the spatial framework of the Biogeographical Regions of Europe (BGRE) as defined by the European Environmental Agency (EEA) on the basis of climate and vegetation. The results obtained show the soil assemblages, including dominant soils and endemic and non-endemic soil minorities, and their respective soil diversity for each BGRE. Most BGRE have dominant soils that mainly reflect the influence of the climatic conditions prevailing in each regional context. Although the definition of the BGRE lacks relevant information on geology, relief and paleogeographic evolution, soil assemblages of most biogeographical regions are idiosyncratic and characterize quite well the European soilscapes. Northern BGRE (i.e. Arctic and Boreal) have low pedotaxa diversity in contrast to the other BGRE. The mountain biome has the highest pedorichness at European as well as at global level. The Atlantic and Mediterranean regions and, to some extent, the Alpine region are mutually related. Most continental soilscapes constitute a mix of typical steppe and forest soils. The Black Sea region, the smallest one of all, has no idiosyncratic soil type, suggesting that it could be considered as an important biodiversity hotspot rather than a genuine biogeographical region. These results are relevant as baseline information for a full inventory of pedodiversity and as an important part of the European natural heritage.

Ethnobiology For A Diverse World Spaces and Natures: Archaeology and the Political Ecology of Modern Cities

Scientific insights are sometimes found in the least likely places. For an ethnobiologist whose research focuses generally on the intersection of culture and biology, the city may seem like the last place to search for answers to complex questions surrounding the relationship between the social and the natural or the material and immaterial. Yet the archaeology of modern cities reveals a complex fabric of spaces whose emergence at the nexus of social and biological forces makes them ideal for examining their interaction. Such investigations are aided by a strong interdisciplinary approach that combines the more traditional study of material culture with the examination of the political ecologies that have shaped the urban landscape. Political ecology informs the work of scholars in a variety of disciplines who seek to transcend the former dichotomous worlds of nature and society in the hopes of forging a new understanding of the intersection of the material and immaterial (e.g., Bennett 2010; Beitl 2012; Collins 2008; Greenberg 2006; Uggla 2010). As the products of human hands, cities are nevertheless an assemblage of hydrologies, soils, animal and plant communities, and landscapes that, over time, develop their own unique ecologies. Using a variety of data sets –historical, material, biological– archaeologists investigating modern cities are able to chronicle both the establishment, and the unfolding changes, that shaped their emergent ecologies. The results provide a provocative comparison with the ideologies and abstract plans that went into the production of these cities. My own research has focused extensively on the production of urban industrial spaces that often involved the purposeful incorporation of natural

Influence of two exotic earthworm species with different foraging strategies on abundance and composition of boreal microarthropods

In North America, many species of European earthworms have been introduced to northern forests. Facilitative or competitive interactions between these earthworm species may result in non-additive effects on native plant and animal species. We investigated the combined versus individual effects of the litter-dwelling earthworm Dendrobaena octaedra Savigny, 1826 and the deep-burrowing species Lumbricus terrestris L., 1758 on microarthropod assemblages from boreal forest soil by conducting a mesocosm experiment. Soil cores from earthworm-free areas of northern Alberta, Canada, were inoculated with D. octaedra alone, L. terrestris alone, both worm species together, or no earthworms. After 4.5 months, microarthropods were extracted from the soil, counted, and identified to higher taxa. Oribatid mites were further identified to family and genus. Abundance of microarthropods was significantly lower in the treatment containing both species than in the no earthworm treatment and the L. terrestris treatment. Oribatida and Prostigmata/Astigmata differed significantly among treatments and were lowest in the treatment containing both earthworm species, followed by the D. octaedra treatment, although post-hoc pairwise comparisons were not significant. Within the Oribatida, composition differed between the control and L. terrestris treatments as compared to the D. octaedra and both-species treatments, with Suctobelbella and Tectocepheus in particular having higher abundances in the control treatment. Effects of the two earthworm species on microarthropods were neither synergistic nor antagonistic. Our results indicate that earthworms can have strong effects on microarthropod assemblages in boreal forest soils. Future research should examine whether these changes have cascading effects on nutrient cycling, microbial communities, or plant growth.

Woodland history in the upper Harz Mountains revealed by kiln site, soil sediment and peat charcoal analyses

Charcoal is abundant in various soils and soil sediments and is basically the result of either natural wildfires or of anthropogenic ignition. Compositions of charcoal assemblages are the result of several taphonomical processes. Beside this, little is known about the influence of charcoal from anthropogenic origin, like charcoal production sites (kiln sites) on soil charcoal assemblages. To elucidate how human charcoal production as well as erosion of the relicts of kiln sites influenced charcoal assemblages in soils and mires, a multi-proxy approach was applied at two transects on the Renneckenberg, a steep slope in the low mountain range Harz, Germany. On this slope, three types of archives (soil/soil sediments, kiln sites and peatland) were investigated each with different methods on a local scale (soil charcoal analyses, kiln site charcoal analyses, peat macro-/micro-charcoal and pollen analysis). The kiln site charcoal records are taxonomically richer in wood taxa than those from colluvial assemblages, especially regarding deciduous tree species. Fagus sylvatica and Acer sp. are rare or absent in the colluvial charcoal assemblages which are dominated by Picea charcoal. At the bottom of the slope, the soil charcoal concentration is very high and indicates strong erosion of charcoal from the upper part of the slope. Significant taxonomical discrepancies between the colluvial and the kiln site charcoal assemblages may be related to different fire intensity throughout the Holocene and to human woodland usage. Additionally, changes in the run-off intensity and fire frequency are detected in the peat macro-charcoal record reflecting vegetation change in the early Holocene. The micro-charcoal content coincides with the main mining phases in the late Holocene and the 9.2 k climatic anomaly.

Phytolith assemblages and opal concentrations from modern soils differentiate temperate grasslands of controlled composition on experimental plots at Cedar Creek, Minnesota

Researchers frequently assume that phytolith assemblages in modern soils reflect composition of recent vegetation because of the direct deposition of silica into the soil, once plants decay. This paper tests this assumption and determines whether temperate grasslands of different composition can be reliably detected based on their silica record in topsoil in a controlled experiment. The differences in total biogenic opal concentration (TBOC) and diversity of morphotypes were assessed in the Biodiversity II experiment (E120) at Cedar Creek Ecosystem Science Reserve, Minnesota, USA, where controlled mixtures of C3 grasses, C4 grasses, legumes, non-legume forbs, and woody shrubs (Quercus) were grown for a period of eight years. The plots have been manually maintained to contain the target species, and thus provide an opportunity to test numerous hypotheses regarding phytolith production patterns under diverse mixtures of plants. Soil samples were obtained from plots representing a variety of functional group mixtures. Pinch soil samples of 20 g from 10 random locations inside each plot were obtained. Phytoliths were extracted from each sample by chemically removing organics and carbonates and using heavy liquid flotation. A chemical dissolution method was used to obtain estimates of TBOC. Morphotypes were counted under a microscope. Morphotypes were analyzed on all plots against each other and against the morphotypes expected in the plants that grow on each plot using ANOVAs, linear regression, PCA and cluster analysis. Average above-ground biomass of expected phytolith producers was weakly but positively correlated with the TBOC values (R2 = 0.42). The morphotype analysis showed that species' composition was most accurately reflected in the phytolith assemblages on grass-dominated plots. For example, it was possible to distinguish C3, C4, or mixed grass-dominated plots from each other. Although the majority of phytoliths were from Poaceae, large shares were also from forbs and woody plants. Plots without any grasses still had some presence of grass phytoliths suggesting limited horizontal translocation and/or inheritance.

Application of the Ludox-QPS method for estimating ciliate diversity in soil and comparison with direct count and DNA fingerprinting

Soil ciliates have advantages in monitoring soil quality after pollution and disturbance. However the potential is limited by the shortcoming of integrating quantitative and qualitative techniques. Here we utilized the Ludox-Quantitative Protargol Stain (Ludox-QPS) method which was originally developed for marine sediment to assess ciliate diversity in soil. The method was tested with three soil samples and compared with a ciliate-specific Denaturing Gradient Gel Electrophoresis (DGGE) and direct count method. The Ludox-QPS method obtained significantly higher number of ciliates with higher taxonomic resolution than the direct count, and revealed higher diversity than the DGGE as well as subsequent gene sequencing. Besides, we evaluated the effects of 2% glutaraldehyde fixative and the QPS preparation on cell size of one species from each of the three dominant ciliate assemblages in soil: colpodids, hypotrichs and haptorids. The experiment indicates a biovolume conversion factor of ∼0.69 for soil ciliates treated with the Ludox-QPS method. The Ludox-QPS method fulfills the enumeration of soil ciliates with good taxonomic resolution and thus promotes the utilization of ciliates in the bioassessment of soil environments.

Spatial and temporal changes of cyanophage communities in paddy field soils as revealed by the capsid assembly protein gene g20

Bacteriophages are ubiquitous in various environments. Our previous study revealed the diversity of the cyanophage community in paddy floodwater. In this study, the phylogeny and genetic diversity of cyanophage communities in paddy field soils were reported. The viral capsid assembly protein gene (g20) of cyanophage was amplified with the primers CPS1 and CPS8 from soil DNA extracted during two different sampling times at three sampling sites in Japan. The sequencing results indicated that about 93% of the clones were g20 genes. In total, 70 clones of g20 genes were obtained in this study, of which 69 clones were of cyanophage origin. As evaluated by g20 sequence assemblages in paddy field soils, the unifrac analyses results indicated that cyanophage communities changed among the sampling sites and times and differed from those communities detected in paddy floodwater. The phylogenetic analysis showed that the g20 sequences in paddy field soils were very diverse and distributed into Clusters α, β and ɛ, as well as four newly formed clusters. Within Clusters β and ɛ, four unique subclusters were formed from the g20 clones that were only observed in this study. These findings suggested that the cyanophage communities in paddy field soils are different from those found in freshwater, marine water and paddy floodwater.

Toward a Theory of Island Pedogeography: Testing the driving forces for pedological assemblages in archipelagos of different origins

The Theory of Island Biogeography has been based on biodiversity studies and used as a powerful predictive tool. Currently pedogeography does not have a similar theoretical construct. Although island biodiversity and biological assemblages have been topics of widespread interest in biogeography, ecology and conservation biology, soil scientists have conducted few studies of pedodiversity and pedological assemblages in archipelagos. Several studies have demonstrated that pedodiversity and biodiversity patterns have striking similarities in very disparate environments and at different scales, thus it is possible to test for a similar construct of island pedogeography. We analyze similarities and differences in the pedosphere for three archipelagos with different origins: (i) oceanic-intra-plate chains islands (Hawaiian Islands), (ii) oceanic-intra-plate cluster islands (Canary Islands), (iii) non-marine land-bridge islands with volcanism associated with plate boundary conditions (Aegean Islands) and (iv) as a comparison, islands in a nonplate boundary setting (the British Isles). In the Canary Islands, we also compiled selected biological, physiographical, geological and climatic data for further analysis of pedodiversity, climatic diversity, geodiversity and biodiversity. Our pedogeographic analysis of the three archipelagos indicates archipelagos of varying origins contain different soil assemblages with plate tectonics as the main driving force. The similarities between pedodiversity and biodiversity are more remarkable than the differences. We tested the hypothesis that soil taxa distributions on island chains can be modelled as a power function similar to the species–area relationship (SAR) proposed by McArthur and Wilson for archipelagos. The SAR functional relationship has been widely corroborated in other biodiversity studies. The same patterns were obtained for pedodiversity and biodiversity in the British Isles, and after that in the Aegean Archipelago. In this study we show similar results in the Canary Islands. Furthermore, in the Canary Archipelago, a strong relationship exists between pedodiversity, biodiversity, climate diversity, habitat heterogeneity and relief. For the Hawaii Archipelago, we did not obtain a statistically significant relationship because soil inventories are not published for the smallest islands and islets. However, Hawaii does have a chronosequence from the older to the younger land units. Overall, the dynamics of the underlying plate tectonic hot spots seems to be the major driving force affecting the various diversity types. Based on these results, we suggest a theoretical proposal of “Island pedogeography” consistent and similar to the Theory of Island Biogeography, in view that the latter one also predicts the pedodiversity of soil assemblages in archipelagos. This study illustrates several possibilities for further research in soil geography.

Influence of geographical location, crop type and crop residue cover on bacterial and fungal community structures

The objective of this study was to evaluate the effects of geographical location, crop type, and residue coverage on soil microbial assemblages in Sherm soil from 30 geographically separate commercial fields in Ochiltree and Moore Counties of Texas. Crop residue coverage was derived from spectral data and used to classify sorghum and wheat fields into high and low crop residue categories. Denaturing gradient gel electrophoresis-polymerase chain reaction (DGGE-PCR) assays employing universal PCR primers that target prokaryotic and eukaryotic ribosomal genes were used to evaluate microbial community structure. An interaction between geographical location, crop type, and crop residue coverage was observed. A 50% similarity level was observed for overall bacterial community structure as determined using 16S data while a 59% similarity was observed for overall fungal community structure using 18S data. For the 16S composite dataset, high overall rates of correct classification (ORCC) were observed based on the user-defined groups of county by crop by residue coverage. A similar result was observed for fungal community structure using primer set FR1GC-FF390. Our data support the hypothesis that there are multiple provinces and multiple habitats that govern the assemblage of free-living taxa within the Moore–Ochiltree County agroecosystem. An ancient microbial assemblage based on historical features was identified and is still visible despite the presence of different crop types and cropping systems (Conventional vs. Conservation). For sorghum and wheat grown in Moore and Ochiltree Counties, a two-province state (Moore and Ochiltree Counties) was defined comprised of four habitats i.e. sorghum and wheat habitats influence by degree of residue coverage. Crop type and residue coverage can affect microbial assemblages within a geographical context.

The Quaternary of the British Isles: factors forcing environmental change

AbstractThis paper considers the processes that have controlled cool temperate latitude terrestrial environments over the last ca 3 Ma, with particular reference to the British Isles. A scheme is proposed that is based on the processes that act on the land over any given period of time and are the product of climate modulated by rock type (the resisting agent) and relief (determined by tectonics and antecedent relief‐forming factors). Climate is generalised in terms of the range and rates of climate change determined by orbital forcing. During precession cycles climate change was small and insolation levels were forced by chemically and biologically driven processes. The period of obliquity cycles is characterised by patterns of climate change in which physical processes became effective and high‐magnitude fluvial and slope processes were reinforced by periglaciation and glaciation in susceptible regions. Eccentricity cycles include climate extremes of longer duration, and glaciation and periglaciation were the major contributors to landscape change, sediment transfer and sediment mixing. These climate‐forced processes produce distinctive landform, sediment and soil assemblages characteristic of particular episodes of Quaternary time. The lags between the successive systems are identified. Copyright © 2010 John Wiley &amp; Sons, Ltd.