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This study investigated how repeated applications of different types of anaerobic digestates and undigested cattle slurry affected the growth responses and nutritional aspects of ryegrass swards (Lolium perenne L.) and soil nutrient concentrations, in a two-season field trial. The treatments included four different types of anaerobic digestate, undigested cattle slurry, nitrogen control (N-control) with calcium ammonium nitrate (CAN) and a no fertiliser control, distributed in a randomised block design with three replicates. The different types of biofertilisers drove a comparable average forage daily growth rate varying between 65 and 79 kg ha−1 day−1 (p > 0.05). Crude protein and neutral or acid detergent fibre of the forage were not influenced by any type of biofertiliser (p > 0.05). Most of the anaerobic digestates led to increases in the level of soil available P and K (p

This study compared the fertiliser effects of different types of liquid anaerobic digestates on the growth of perennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.), and on soil's primary plant macronutrients and microbial abundance. A factorial design with seven fertilisers and one control (five liquid anaerobic digestates, undigested cattle slurry, calcium ammonium nitrate (CAN) 27% N, and no fertiliser) and four plant schemes (monocultures of perennial ryegrass and white clover, a mix of both, and bare soil) were tested. Plant (forage yield, leaf area index (LAI), canopy height and root mass) and soil (concentrations of total N, Morgan's extracted P and K) responses were measured, as well as soil bacterial/archaeal (16S) and fungal (18S) gene copy numbers (GCN). Digestates and cattle slurry with different chemical compositions, when balanced in terms of the quantity of dry matter applied, had comparable forage yield responses (p > 0.05), with higher yields than CAN mostly observed in ryegrass and mixed vegetation (p

Implementation of guidelines to reduce the amount of biodegradable municipal waste (BMW) sent to landfill has created a need in the waste-management industry to investigate possible methods of accelerating biostabilisation of residual BMW. The effect of commercially feasible manipulations (lime and green waste (GW)) on the rate of biostabilisation of the fine (2 kg DM−1 h−1 recommended by the Irish compost standard. Biostabilised wastes met recommendations for source-segregated compost for pH (6-8) and pathogens ( E. coli and Salmonella), but not heavy metals, indicating their unsuitability for uses other than landfill cover. Levels of AOA genes (log 3–6 g−1 DM) were higher than AOB (log 1–6 g−1 DM, indicating AOA may contribute more to potential ammonia oxidation in residual BMW composting.

This study aimed to quantity total numbers of bacteria, fungi and archaea in different types of commercial liquid anaerobic digestates, and to identify common patterns in their microbial numbers post-digestion and possible implications of their use as biofertiliser. Relationships between microbial numbers and physical-chemical traits of the digestates were also investigated. Quantification was performed using culturable and molecular (quantitative PCR) approaches. Bacterial and fungal CFUs ranged up to five orders of magnitude (105 to 1010; 0 to 105 g-1 DW, respectively) between different types of anaerobic digestates. Bacterial, archaeal and fungal gene copy numbers (GCN) varied by two orders of magnitude (108 to 1010; 107 to 109; 104 to 106 g-1 DW, respectively) between digestates. All microbial variables analysed showed significant differences between the different types of anaerobic digestate investigated (p 4 CFU g-1 DW) were much lower than for bacteria (2.23 × 109 CFU g-1 DW). Gene copy numbers were highest for bacteria (16S) (1.09 × 1010 g-1 DW), followed by archaea (16S) (5.87 × 108 g-1 DW), and fungi (18S) (1.77 × 106 g-1 DW). Liquid anaerobic digestates were predominantly dominated by bacteria, followed by archaeal and fungal populations. At 50% similarity level, the microbial profiles of the eleven anaerobic digestates tested separated into just two groups, indicating a broad relative degree of similarity in terms of microbial numbers. Higher bacterial (16S) GCN was associated with low OM and C/N ratio in digestates.

Anaerobic digestates, which are co-products from biogas production, have been recognised as potential biofertilisers for their benefits in nutrient recovery and recycling of different types of organic wastes. Due to the increasing number of different types of organic wastes being used to produce biogas, it is necessary to identify how different types of anaerobic digestates vary in their physical-chemical traits, and how these can impact upon their use as fertilisers. In addition, safe land spreading of anaerobic digestates must be within recommended limits for potentially toxic elements (PTEs) and pathogens. This study analysed physical-chemical traits, phytotoxicity, PTEs and indicator pathogens in a set of eleven different commercial liquid anaerobic digestates from Ireland and the UK, and compared them to the Irish draft standard for digestate. Liquid anaerobic digestates exhibited significant differences (P

Following a pine beetle epidemic in British Columbia, Canada, we investigated the effect of fire severity on rhizosphere soil chemistry and ectomycorrhizal fungi (ECM) and associated denitrifying and nitrogen (N)-fixing bacteria in the root systems of regenerating lodgepole pine seedlings at two site types (wet and dry) and three fire severities (low, moderate, and high). The site type was found to have a much larger impact on all measurements than fire severity. Wet and dry sites differed significantly for almost all soil properties measured, with higher values identified from wet types, except for pH and percent sand that were greater on dry sites. Fire severity caused few changes in soil chemical status. Generally, bacterial communities differed little, whereas ECM morphotype analysis revealed ectomycorrhizal diversity was lower on dry sites, with a corresponding division in community structure between wet and dry sites. Molecular profiling of the fungal ITS region confirmed these results, with a clear difference in community structure seen between wet and dry sites. The ability of ECM fungi to colonize seedlings growing in both wet and dry soils may positively contribute to subsequent regeneration. We conclude that despite consecutive landscape disturbances (mountain pine beetle infestation followed by wildfire), the “signature” of moisture on chemistry and ECM community structure remained pronounced.

Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2–5 m scale (P < 0.05), whereas AOA communities were dependent at the ∼1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases.

Understanding the links between plant diversity and soil communities is critical to disentangling the mechanisms by which plant communities modulate ecosystem function. Experimental plant communities varying in species richness, evenness, and density were established using a response surface design and soil community properties including bacterial and archaeal abundance, richness, and evenness were measured. The potential to perform a representative soil ecosystem function, oxidation of ammonium to nitrite, was measured via archaeal and bacterial amoA genes. Structural equation modeling was used to explore the direct and indirect effects of the plant community on soil diversity and potential function. Plant communities influenced archaea and bacteria via different pathways. Species richness and evenness had significant direct effects on soil microbial community structure, but the mechanisms driving these effects did not include either root biomass or the pools of carbon and nitrogen available to the soil microbial community. Species richness had direct positive effects on archaeal amoA prevalence, but only indirect impacts on bacterial communities through modulation of plant evenness. Increased plant evenness increased bacterial abundance which in turn increased bacterial amoA abundance. These results suggest that plant community evenness may have a strong impact on some aspects of soil ecosystem function. We show that a more even plant community increased bacterial abundance, which then increased the potential for bacterial nitrification. A more even plant community also increased total dissolved nitrogen in the soil, which decreased the potential for archaeal nitrification. The role of plant evenness in structuring the soil community suggests mechanisms including complementarity in root exudate profiles or root foraging patterns.

Petroleum hydrocarbon (PHC) contamination is becoming more common in boreal forest soils. However, linkages between PHC biodegradation and microbial community dynamics in the mycorrhizosphere of boreal forest soils are poorly understood. Seedlings (lodgepole pine, paper birch, lingonberry) were established in reconstructed soil systems, consisting of an organic layer (mor humus, coarse woody debris, or previously oil-contaminated mor humus) overlying mineral (Ae, Bf) horizons. Light crude oil was applied to the soil surface after 4 months; systems were destructively sampled at 1 and 16 weeks following treatment. Soil concentrations of four PHC fractions were determined using acetone– hexane extraction followed by gas chromatography – flame ionization detection analysis. Genotypic profiles of root-associated bacterial communities were generated using length heterogeneity-PCR of 16S rDNA. Most plant–soil treatments showed significant loss in the smaller fraction PHCs indicating an inherent capacity for biodegradation. Concentrations of total PHCs declined significantly only in planted (pine-woody debris and birch-humus) systems (averaging 59% and 82% loss between 1 and 16 weeks respectively), reinforcing the importance of the mycorrhizosphere for enhancing microbial catabolism. Bacterial community structure was correlated more with mycorrhizosphere type and complexity than with PHC contamination. However, results suggest that communities in PHC-contaminated and pristine soils may become distinct over time.

The effect of the addition of synthetic sheep urine (SSU) and plant species on the bacterial community composition of upland acidic grasslands was studied using a microcosm approach. Low, medium, and high concentrations of SSU were applied to pots containing plant species typical of both unimproved ( Agrostis capillaris ) and agriculturally improved ( Lolium perenne ) grasslands, and harvests were carried out 10 days and 50 days after the addition of SSU. SSU application significantly increased both soil pH ( P < 0.005), with pH values ranging from pH 5.4 (zero SSU) to pH 6.4 (high SSU), and microbial activity ( P < 0.005), with treatment with medium and high levels of SSU displaying significantly higher microbial activity (triphenylformazan dehydrogenase activity) than treatment of soil with zero or low concentrations of SSU. Microbial biomass, however, was not significantly altered by any of the SSU applications. Plant species alone had no effect on microbial biomass or activity. Bacterial community structure was profiled using bacterial automated ribosomal intergenic spacer analysis. Multidimensional scaling plots indicated that applications of high concentrations of SSU significantly altered the bacterial community composition in the presence of plant species but at different times: 10 days after application of high concentrations of SSU, the bacterial community composition of L. perenne -planted soils differed significantly from those of any other soils, whereas in the case of A. capillaris -planted soils, the bacterial community composition was different 50 days after treatment with high concentrations of SSU. Canonical correspondence analysis also highlighted the importance of interactions between SSU addition, plant species, and time in the bacterial community structure. This study has shown that the response of plants and bacterial communities to sheep urine deposition in grasslands is dependent on both the grass species present and the concentration of SSU applied, which may have important ecological consequences for agricultural grasslands.

This study exploited the contrasting major element chemistry of adjacent, physically separable crystals of framework and sheet silicates in a pegmatitic granite to investigate the mineralogical influences of fungal community structure on mineral surfaces. Large intact crystals of variably weathered muscovite, plagioclase, K-feldspar, and quartz were individually extracted, together with whole-rock granite. Environmental scanning electron microscopy (ESEM) revealed a diversity of fungal structures, with microcolonial fungi and fungal hyphae clearly visible on surfaces of all mineral types. Fungal automated ribosomal intergenic spacer analysis (FARISA) was used to generate a ribotype profile for each mineral sample and a randomization test revealed that ribotype profiles, or community fingerprints, differed between different mineral types. Canonical correspondence analysis (CCA) revealed that mineral chemistry affected individual fungal ribotypes, and strong relationships were found between certain ribotypes and particular chemical elements. This finding was further supported by analysis of variance (ANOVA) of the 16 most abundant ribotypes within the community. Significantly, individual ribotypes were largely restricted to single mineral types and ribotypes clustered strongly on the basis of mineral type. CCA also revealed that Al, Si, and Ca had a significant impact on fungal community structure within this system. These results show that fungal community structure was driven by the chemical composition of mineral substrates, indicating selective pressure by individual chemical elements on fungal populations in situ.

Floristically diverse Nardo-Galion upland grasslands are common in Ireland and the UK and are valuable in agricultural, environmental and ecological terms. Under improvement (inputs of lime, fertiliser and re-seeding), they convert to mesotrophic grassland containing very few plant species. The effects of upland grassland improvement and seasonality on soil microbial communities were investigated at an upland site. Samples were taken at five times in one year in order to observe seasonal trends, and bacterial community structure was monitored using automated ribosomal intergenic spacer analysis (ARISA), a DNA-fingerprinting approach. Differences in soil chemistry and bacterial community structure between unimproved and improved grassland soils were noted. Season was also found to cause mild fluctuations in bacterial community structure, with soil samples from colder months (October and December) more correlated with change in ribotype profiles than samples from warmer months. However, for the majority of seasons clear differences in bacterial community structures from unimproved and improved soils could be seen, indicating seasonal influences did not obscure effects associated with improvement.

A microcosm-based approach was used to study impacts of plant and chemical factors on the fungal community structure of an upland acidic grassland soil. Seven plant species typical of both unimproved and fertilized grasslands were either left unamended or treated with lime, nitrogen or lime plus nitrogen. Fungal community structure was assessed by a molecular approach, fungal automated ribosomal intergenic spacer analysis (FARISA), while fungal biomass was estimated by measuring soil ergosterol content. Addition of nitrogen (with or without lime) had the largest effect, decreasing soil pH, fungal biomass and fungal ribotype number, but there was little corresponding change in fungal community structure. Although different plant species were associated with some changes in fungal biomass, this did not result in significant differences in fungal community structure between plant species. Addition of lime alone caused no changes in fungal biomass, ribotype number or community structure. Overall, fungal community structure appeared to be more significantly affected through interactions between plant species and chemical treatments, as opposed to being directly affected by changes in individual improvement factors. These results were in contrast to those found for the bacterial communities of the same soils, which changed substantially in response to chemical (lime and nitrogen) additions.

Fungi can be found in almost any environment, and play important roles in ecosystem processes such as nutrient cycling and degradation. Despite their importance, the vast majority of fungi have not yet been isolated and identified. Due to the difficulties inherent in culture-based methods, fungal ecologists have turned to community fingerprinting techniques, which utilise signal molecules to profile the fungal members of an environmental sample without culturing. Commonly used signal molecules include chitin, ergosterol, membrane lipids, and nucleic acids. Several DNA-based fingerprinting methods have been successfully applied to fungal communities, including D/TGGE (denaturing/temperature gradient gel electrophoresis), SSCP (single-stranded conformational polymorphism), RISA (ribosomal intergenic spacer analysis), and T-RFLP (terminal restriction length fragment polymorphism). These techniques allow the fungal ecologist to rapidly profile fungal populations in an ecosystem, without the need for laborious culturing or cloning.

Agricultural improvement of seminatural grasslands has been shown to result in changes to plant and microbial diversity, with consequences for ecosystem functioning. A microcosm approach was used to elucidate the effects of two key components of agricultural improvement (nitrogen addition and liming) on ammonia-oxidising bacterial (AOB) communities in an upland grassland soil. Plant species characteristic of unimproved and improved pastures (A. capillarisandL. perenne) were planted in microcosms, and lime, nitrogen (NH4NO3), or lime plus nitrogen added. The AOB community was profiled using terminal restriction fragment length polymorphism (TRFLP) of theamoAgene. AOB community structure was largely altered byNH4NO3addition, rather than liming, although interactions between nitrogen addition and plant species were also evident. Results indicate that nitrogen addition drives shifts in the structure of key microbial communities in upland grassland soils, and that plant species may play a significant role in determining AOB community structure.

Wildfire and logging are common disturbances in the forests of northwestern North America, causing changes in soil chemistry and microbiology, including fungal and nitrogen-cycling bacterial communities. These organisms play key roles in nutrient cycling, and affect the regeneration of tree seedlings after disturbance. We studied the effects of wildfire and logging on fungal and nitrogen-cycling communities in the rhizosphere of 16 month-old Douglas-fir seedlings as they regenerated in burned and logged soils. Seeds were planted against root windows that were set up vertically in the soil, with a removable front panel used to access the seedling rhizosphere soil surface. Windows were established in control, lightly burned, and severely burned plots, as well as two types of logged plots (clearcut and screefed clearcut). Soil scrapings from the root window–soil interface were taken and the structure of fungal and nitrogen-cycling communities was resolved using length-heterogeneity PCR (LH-PCR) of fungal nuclear ribosomal RNA genes, and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and nosZ genes. We found striking differences in the community structure of fungal, denitrifying, and N-fixing communities in response to burning and logging. With the exception of clearcut and screefed clearcut, which were generally similar, each treatment had a unique impact on community structure for these genes. Burning and logging also impacted the relative richness and evenness of these communities. Fungal relative richness and evenness increased in response to logging and severe burning, while denitrifier relative richness and evenness increased in all disturbance treatments, and N-fixing bacterial relative richness and evenness decreased in response to burning. The greatest differences in microbial community structure, relative richness, and evenness were found in the comparisons of lightly burned and logged treatments. The results suggest that the presence of an intact forest floor influences soil microbial communities less than the presence of living trees.

Seasonal and management influences on the fungal community structure of two upland grassland soils were investigated. An upland site containing both unimproved floristically diverse (U4a) and improved mesotrophic (MG7b) grassland types was selected. Samples from both grassland types were taken at five times in one year. Soil fungal community structure was assessed using fungal automated ribosomal intergenic spacer analysis (ARISA), a DNA-profiling approach. A grassland management regime was found to strongly affect fungal community structure, with fungal ARISA profiles from unimproved and improved grassland soils differing significantly. The number of fungal ribotypes found was higher in unimproved than improved grassland soils, providing evidence that improvement may reduce the suitability of upland soil as a habitat for specific groups of fungi. Seasonal influences on fungal community structure were also noted, with samples taken in autumn (October) more correlated with change in ribotype profiles than samples from other seasons. However, seasonal variation did not obscure the measurement of differences in the fungal community structure that were due to agricultural improvement, with canonical correspondence analysis indicating grassland type had a stronger influence on fungal profiles than did season.Key words: upland grasslands, fungal automated ribosomal intergenic spacer analysis, seasonality, improvement, canonical correspondence analysis.

Changes in soil microbial community structure due to improvement are often attributed to concurrent shifts in floristic community composition. The bacterial and fungal communities of unimproved and semi-improved (as determined by floristic classification) grassland soils were studied at five upland sites on similar geological substrata using both broad-scale (microbial activity and fungal biomass) and molecular [terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA)] approaches. It was hypothesized that microbial community structure would be similar in soils from the same grassland type, and that grassland vegetation classifications could thus be used as predictors of microbial community structure. Microbial community measurements varied widely according to both site and grassland type, and trends in the effect of grassland improvement differed between sites. These results were consistent with those from similar studies, and indicated that floristic community composition was not a stable predictor of microbial community structure across sites. This may indicate a lack of correlation between grassland plant composition and soil microbial community structure, or that differences in soil chemistry between sites had larger impacts on soil microbial populations than plant-related effects.

A microcosm-based approach was used to study impacts of plant and chemical factors on the bacterial community structure of an upland acidic grassland soil. Seven perennial plant species typical of both natural, unimproved ( Nardus stricta , Agrostis capillaris , Festuca ovina and F. rubra ) and fertilized, improved ( Holcus lanatus, Lolium perenne and Trifolium repens ) grasslands were either left unamended or treated with lime, nitrogen, or lime plus nitrogen in a 75-day glasshouse experiment. Lime and nitrogen amendment were shown to have a greater effect on microbial activity, biomass and bacterial ribotype number than plant species. Liming increased soil pH, microbial activity and biomass, while decreasing ribotype number. Nitrogen addition decreased soil pH, microbial activity and ribotype number. Addition of lime plus nitrogen had intermediate effects, which appeared to be driven more by lime than nitrogen. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed that lime and nitrogen addition altered soil bacterial community structure, while plant species had little effect. These results were further confirmed by multivariate redundancy analysis, and suggest that soil lime and nitrogen status are more important controllers of bacterial community structure than plant rhizosphere effects.