Vadakattu V. S. R. Gupta

Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing.

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils ‘suppressive’ or ‘non-suppressive’ for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.

Environmental impact of conventional and Bt insecticidal cotton expressing one and two Cry genes in Australia

Genetically modified Bt cotton, expressing the Cry1Ac protein for specific insecticidal activity against economically significant lepidopteran pests, has been available commercially in Australia since 1996. This technology has been improved and superseded by the addition of a second gene, allowing new varieties to express both the Cry1Ac the Cry2Ab proteins. Bt cotton offers several advantages to the grower, mainly through reduced insecticide spray requirements. The environmental benefits of reduced insecticide usage are assessed in this paper using the environmental impact quotient (EIQ). The assessment included consideration of the impact of the expressed transgenic proteins Cry1Ac and Cry2Ab. EIQ values of the Cry1Ac and Cry2Ab proteins were calculated at 9.9 and 7.9, respectively. Bt protein expression, plant biomass, insecticide application records, constituent of active ingredient, and insecticide EIQ values were used to produce an environmental impact (EI) value for insecticide use (kg a.i./ha) for conventional non-GM and single- and 2-gene Bt cotton for the 1997–98 to 2003–04 seasons. Inclusion of the Cry proteins in the assessment increased the EI values for Bt cotton by only 2%. The average insecticide EI value, for 2002–03 and 2003–04 seasons, for conventional cotton was 135 kg a.i./ha, whereas for the 2-gene Bt variety it was only 28 kg a.i./ha. Results of the EI evaluation indicate that, due to changes in insecticidal choice and reduction in usage, there was a reduction of >64% in EI from growing Bt cotton compared with conventional non-GM cotton in Australia.

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

BackgroundMicrobial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function.FindingsBASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project’s data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the ‘Atlas of Living Australia’.ConclusionsDeveloped within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.

Principles and Management of Soil Biological Factors for Sustainable Rainfed Farming Systems

Soil microflora and fauna are important for organic matter decomposition and hence nutrient cycling, organic matter turnover, disease incidence and suppression, agrochemical degradation and soil structure. Soil moisture, temperature and availability of energy source (carbon) determine the activity of these organisms. Biological activity and plant growth must be synchronised for optimum production. Control of soil-borne root pathogens is important in maximising water use efficiency. The beneficial influences of soil biota include nitrogen fixation, nutrient cycling and supply, improved soil structure, promotion of plant and root growth, and disease control or suppression. Detrimental influences include those of root pathogens and deleterious rhizobacteria.

Potential for non-symbiotic N2-fixation in different agroecological zones of southern Australia

Nitrogen fixation by symbiotic and non-symbiotic bacteria can be a significant source of nitrogen in cropping systems. However, contributions from non-symbiotic nitrogen fixation (NSNF) are dependent on available carbon in the soil and environmental conditions (soil moisture and temperature). In Australia, measurements of NSNF have been made in the field by quantifying nitrogenase activity. These studies have included determinations of the moisture and temperature requirements for NSNF and for crop residue decomposition that supplies carbon to NSNF bacteria. Other studies have determined the N input by NSNF using N budget calculations. These data together with information about carbon supply and environmental conditions were used to estimate potential NSNF in the cropping zones of southern Australia. Using the ArcviewGIS Spatial Analyst (v3.1), maps of Australia showing estimates of NSNF in different cropping zones as determined by rainfall and temperature or carbon availability were generated. In Western Australia (represented by Wongan Hills) and South Australia (represented by Avon), where summers are dry, estimates of NSNF were generally low (10–15 kg N/ha from January to June) due to limitations of soil moisture. In New South Wales, particularly in the north where summer rainfall patterns develop (represented by Gunnedah), the warm, moist conditions produced higher estimates of NSNF (totaling 32–38 kg N/ha from January to June). In this region, the majority of estimated NSNF occurred in January and February leading to the depletion of carbon supplies and reduced NSNF in autumn (March–June). Information about potential supplies of N from NSNF across the cropping zones should be useful for researchers to select and study areas that are most likely to benefit from NSNF. It should also help agronomists and extension officers explain changes in N status within paddocks or within specific farming systems and to provide more accurate advice on N fertiliser requirements, particularly in low-input farming systems.

Soil biota and crop residue decomposition during summer and autumn in south-western Australia.

We determined the impact of the presence of lupin and wheat residues on decomposer fauna and measured the decomposition rate of these residues during summer and autumn in paddocks previously cropped with either wheat or lupin at East Beverley in Western Australia. Populations of various groups of decomposer soil biota and nitrogen dynamics (immobilization and mineralization) were measured using litterbags. In December 1996, litterbags with lupin residues were placed on soil after a lupin crop while litterbags with wheat residues were placed on soil that had grown wheat in the previous growing season. From January until the end of June 1997, substrate-induced respiration, protozoa, nematodes and microarthropods and mass loss and carbon and nitrogen contents of the remaining residues were measured at regular intervals. During the 6 months of incubation, 15‐20% of mass loss occurred for both wheat and lupin residues. Decomposition rates for lupin and wheat were 0.0013 and 0.0011 day 1 , respectively. The largest decrease in residue mass occurred after the first major rainfall, probably due to the loss of water-soluble compounds. Between days 60 and 130 (March to the beginning of May) the loss in mass of both residue types was gradual, coinciding with large numbers of microfauna. Mass loss of residues was minimal during the period between 126 and 188 days when large numbers of mesofauna were observed. A significant loss in nitrogen was only observed for the lupin residues, whereas net immobilization of nitrogen occurred with the wheat residues during this 6-month study. At the beginning of the study, substrate-induced respiration was higher for the lupin residues suggesting that microorganisms colonized the lupin more extensively than the wheat residues. In June, microbial biomass on lupin and wheat residues was similar. Higher nematode, amoebae and ciliate abundances on the lupin residues might have prevented a further increase in the microbial biomass. Measurable populations of protozoa and nematodes were observed in the first sampling date in March, whereas quantifiable numbers of microarthropods only appeared in May, 4 months after placement of the litterbags in the field. Prostigmatic mites were abundant on the wheat residues, while Collembola were the most abundant microarthropods on the lupin residues. Food quality and predatory pressures may have affected the succession of different soil biota communities on the lupin and wheat residue.

Tillage practices altered labile soil organic carbon and microbial function without affecting crop yields

A 7-year tillage experiment was conducted on a deep sand in the central wheat belt of Western Australia between 1998 and 2004 to evaluate the impact of tillage intensity [no-tillage (NT), conservation tillage (CT), and rotary tillage (RT)] on soil organic matter, microbial biomass and function, and crop yields in a wheat–lupin rotation. A fourth treatment (subterranean clover pasture, Pasture) with least soil disturbance was included as a comparison. By March 2004, total soil carbon (C) in NT and CT increased by 4.4 and 2.6 t/ha, respectively, to an average of 17.6 t/ha in the top 0.1 m of the soil profile. There was a loss of total soil C in RT (–0.5 t/ha), which was significant compared with the other 2 tillage treatments. Total soil C and nitrogen (N) contents in the pasture treatment were similar to those in NT and CT at the end of the experiment. Labile fractions of soil C responded more rapidly to tillage practice, with significant reductions by 2001 in light fraction C and dissolved organic C in the RT treatment compared with the other 3 treatments. The effect of RT on biology and function was seen early in the experiment and, compared with Pasture, NT, and CT, intense tillage in RT significantly reduced microbial biomass and cellulase activity in the surface 0.05 m by the third year of the experiment. However, at a depth of 0.05–0.10 m there were no significant differences between treatments. Grain yields in NT, CT, and RT were unaffected by tillage except in 2003, when lupin yield under RT (1.6 t/ha) was significantly less than under NT (2.0 t/ha) and CT (1.9 t/ha). Minimal differences between NT and CT are a reflection of the minimum disturbance in the CT treatment, although there were significant differences between CT and NT in microbial indices such as microbial quotient and metabolic quotient, suggesting a future divergence of these treatments.

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.

Effects of banded ammonia and urea fertiliser on soil properties and the growth and yield of wheat

Abstract. Experiments conducted over three seasons in southern New South Wales tested the effects of concentrating anhydrous ammonia (AA) and urea fertiliser in bands occupying ∼3.5% of the topsoil volume. Yield responses to applied nitrogen (N) were small or negative in a drought but larger (17 kg grain kg–1 N fertiliser) in favourable seasons. There was no consistent difference between AA and urea effects on yield, grain protein or efficiency of fertiliser-N recovery, and there were no consistent differences arising from banding depth or application time. Gaseous loss of ammonia to the atmosphere was negligible from urea granules or AA injected into the soil as gas or liquid. Soil ammonium concentration was >700 μg N g–1 in bands of ∼5 cm diameter when measured 6 days after AA application but halved within 5 weeks due to nitrification. Within 1 day of banding AA or urea at sowing, pHwater in the bands rose from 6 to 8.5, leading to transient changes in microbial activity and populations. Immediately after banding, microbial biomass carbon and numbers of protozoa fell by about half, but numbers of ammonia- and nitrite-oxidisers were unchanged. Five weeks later, microbial biomass carbon and protozoa had partly recovered whereas numbers of ammonia- and nitrite-oxidisers increased 5–10-fold. After 7 months, there was a small reduction in microbial diversity in the bands, shown by analysis of fatty acid methyl esters. Seedling growth was slower where N fertiliser was applied in concentrated bands than when mixed throughout the topsoil, supporting previous research showing that roots avoid bands of highly concentrated ammonium. Banding thus provided a slow-release form of N to wheat crops, thereby reducing excessive seedling growth and the risks of haying-off.

Quantifying the Sensitivity of Soil Microbial Communities to Silver Sulfide Nanoparticles Using Metagenome Sequencing

Soils are a sink for sulfidised-silver nanoparticles (Ag2S-NPs), yet there are limited ecotoxicity data for their effects on microbial communities. Conventional toxicity tests typically target a single test species or function, which does not reflect the broader community response. Using a combination of quantitative PCR, 16S rRNA amplicon sequencing and species sensitivity distribution (SSD) methods, we have developed a new approach to calculate silver-based NP toxicity thresholds (HCx, hazardous concentrations) that are protective of specific members (operational taxonomic units, OTUs) of the soil microbial community. At the HC20 (80% of species protected), soil OTUs were significantly less sensitive to Ag2S-NPs compared to AgNPs and Ag+ (5.9, 1.4 and 1.4 mg Ag kg-1, respectively). However at more conservative HC values, there were no significant differences. These trends in OTU responses matched with those seen in a specific microbial function (rate of nitrification) and amoA-bacteria gene abundance. This study provides a novel molecular-based framework for quantifying the effect of a toxicant on whole soil microbial communities while still determining sensitive genera/species. Methods and results described here provide a benchmark for microbial community ecotoxicological studies and we recommend that future revisions of Soil Quality Guidelines for AgNPs and other such toxicants consider this approach.