The influence of soil properties on the structure of bacterial and fungal communities across land-use types

Land-use change can have significant impacts on soil conditions and microbial communities are likely to respond to these changes. However, such responses are poorly characterized as few studies have examined how specific changes in edaphic characteristics do, or do not, influence the composition of soil bacterial and fungal communities across land-use types. Soil samples were collected from four replicated (n = 3) land-use types (hardwood and pine forests, cultivated and livestock pasture lands) in the southeastern US to assess the effects of land-use change on microbial community structure and distribution. We used quantitative PCR to estimate bacterial–fungal ratios and clone libraries targeting small-subunit rRNA genes to independently characterize the bacterial and fungal communities. Although some soil properties (soil texture and nutrient status) did significantly differ across land-use types, other edaphic factors (e.g., pH) did not vary consistently with land-use. Bacterial–fungal ratios were not significantly different across the land-uses and distinct land-use types did not necessarily harbor distinct soil fungal or bacterial communities. Rather, the composition of bacterial and fungal communities was most strongly correlated with specific soil properties. Soil pH was the best predictor of bacterial community composition across this landscape while fungal community composition was most closely associated with changes in soil nutrient status. Together these results suggest that specific changes in edaphic properties, not necessarily land-use type itself, may best predict shifts in microbial community composition across a given landscape. In addition, our results demonstrate the utility of using sequence-based approaches to concurrently analyze bacterial and fungal communities as such analyses provide detailed phylogenetic information on individual communities and permit the robust assessment of the biogeographical patterns exhibited by soil microbial communities.     

Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties

The response of soil microbial communities following changes in land-use is governed by multiple factors. The objectives of this study were to investigate (i) whether soil microbial communities track the changes in aboveground vegetation during succession; and (ii) whether microbial communities return to their native state over time. Two successional gradients with different vegetation were studied at the W. K. Kellogg Biological Station, Michigan. The first gradient comprised a conventionally tilled cropland (CT), mid-succession forest (SF) abandoned from cultivation prior to 1951, and native deciduous forest (DF). The second gradient comprised the CT cropland, early-succession grassland (ES) restored in 1989, and long-term mowed grassland (MG). With succession, the total microbial PLFAs and soil microbial biomass C consistently increased in both gradients. While bacterial rRNA gene diversity remained unchanged, the abundance and composition of many bacterial phyla changed significantly. Moreover, microbial communities in the relatively pristine DF and MG soils were very similar despite major differences in soil properties and vegetation. After >50 years of succession, and despite different vegetation, microbial communities in SF were more similar to those in mature DF than in CT. In contrast, even after 17 years of succession, microbial communities in ES were more similar to CT than endpoint MG despite very different vegetation between CT and ES. This result suggested a lasting impact of cultivation history on the soil microbial community. With conversion of deciduous to conifer forest (CF), there was a significant change in multiple soil properties that correlated with changes in microbial biomass, rRNA gene diversity and community composition. In conclusion, history of land-use was a stronger determinant of the composition of microbial communities than vegetation and soil properties. Further, microbial communities in disturbed soils apparently return to their native state with time.     

Compartmentalization of the soil animal food web as indicated by dual analysis of stable isotope ratios (N/N and C/C)

The soil animal food web has become a focus of recent ecological research but trophic relationships still remain enigmatic for many taxa. Analysis of stable isotope ratios of N and C provides a powerful tool for disentangling food web structure. In this study, animals, roots, soil and litter material from a temperate deciduous forest were analysed. The combined measurement of δ¹⁵N and δ¹³C provided insights into the compartmentalization of the soil animal food web. Leaf litter feeders were separated from animals relying mainly on recent belowground carbon resources and from animals feeding on older carbon. The trophic pathway of leaf litter-feeding species appears to be a dead end, presumably because leaf litter feeders (mainly diplopods and oribatid mites) are unavailable to predators due to large size and/or strong sclerotization. Endogeic earthworms that rely on older carbon also appear to exist in predator-free space. The data suggest that the largest trophic compartment constitutes of ectomycorrhizal feeders and their predators. Additionally, there is a smaller trophic compartment consisting of predators likely feeding on enchytraeids and potentially nematodes.     

A new framework of spatial targeting for single-species conservation planning

Context

Organisations acting to conserve and protect species across large spatial scales prioritise to optimise use of resources. Spatial conservation prioritization tools typically focus on identifying areas containing species groups of interest, with few tools used to identify the best areas for single-species conservation, in particular, to conserve currently widespread but declining species.

Objective

A single-species prioritization framework, based on temporal and spatial patterns of occupancy and abundance, was developed to spatially prioritize conservation action for widespread species by identifying smaller areas to work within to achieve predefined conservation objectives.

Methods

We demonstrate our approach for 29 widespread bird species in the UK, using breeding bird atlas data from two periods to define distribution, relative abundance and change in relative abundance. We selected occupied 10-km squares with abundance trends that matched species conservation objectives relating to maintaining or increasing population size or range, and then identified spatial clusters of squares for each objective using a Getis-Ord-Gi* or near neighbour analysis.

Results

For each species, the framework identified clusters of 20-km squares that enabled us to identify small areas in which species recovery action could be prioritized.

Conclusions

Our approach identified a proportion of species’ ranges to prioritize for species recovery. This approach is a relatively quick process that can be used to inform single-species conservation for any taxa if sufficiently fine-scale occupancy and abundance information is available for two or more time periods. This is a relatively simple first step for planning single-species focussed conservation to help optimise resource use.

     

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.

     

Global Dryland Ecosystem Programme (Global-DEP): Australasian consultation report

Journal of Soils and Sediments -     

Changes in phosphorus fractions in three tropical soils amended with corn cob and rice husk biochars

ABSTRACT

The formation of phosphorus (P) compounds including iron-P, aluminum-P and calcium-P in highly weathered tropical soils can be altered upon biochar addition. We investigated the effect of corn cob biochar (CC) and rice husk biochar (RH) pyrolyzed at three temperatures (300°C, 450°C and 650°C) on phosphorus (P) fractions of three contrasting soils. A 90d incubation study was conducted by mixing biochar with soil at a rate of 1% w/w and at 70% field capacity. Sequential P fraction was performed on biochar, soil and soil-biochar mixtures. Increase in most labile P (resin-P_i, NaHCO₃-P_i) and organic P fraction (NaHCO₃-P_o + NaOH-P_o) in CC and RH biochars were inversely related to increasing temperature. HCl-P_i and residual P increased with increasing temperature. Interaction of CC and RH with soils resulted in an increase in most labile P as well as moderately labile P (NaOH-P_i) fractions in the soils. CC increased most labile P in the soils more than RH. The increase in most labile P fraction in soils was more significant at relatively lower temperatures (300°C and 450°C) than 650°C. However, the increase in HCl-P_i and residual P of the soils was more predominant at high temperature (650°C). The study suggested that biochar pyrolyzed at 300–450°C could be used to increase P bioavailability in tropical soils.     

Transendoscopic biopsy of the horse's airway mucosa

Transtracheal wash and bronchoalveolar lavage are diagnostic techniques that have been adopted from human medicine for monitoring inflammatory changes in the airway of the horse. Transendoscopic biopsy has also proven to be a valuable tool for obtaining samples of the airway mucosa in human patients. A transendoscopic technique was developed in this study for obtaining a respiratory mucosal biopsy from standing, sedated horses. Six normal adult horses were sampled at eight-week intervals for a total of three sample periods. Horses were monitored for adverse effects of the technique and none were noted. Sample sites were completely healed after eight weeks with no gross or histologic abnormalities. Biopsy samples were 3 to 4 millimeters in diameter, and 17 of 18 samples provided interpretable histological sections. Methods for handling, staining and evaluating tissue were also developed. The results of this study demonstrated that airway mucosal biopsy is a safe, repeatable technique that can be performed in the sedated, standing horse.