Key physicochemical factors associated with microbial community composition and functions in Australian agricultural soils were identified. Soils from seven field sites, with varying long-term ...agricultural management regimes, were characterised physicochemically, on the basis of their bacterial and fungal community structures (using PCR-DGGE), and by assessing potential catabolic functions (MicroResp™). Soil type, rather than agricultural management practice, was the key determinant of microbial community structure and catabolic function (
P<0.05). Following multivariate analysis, soil pH was identified as the key habitat-selective physicochemical soil property associated with variation in biological diversity and profiles of organic substrate utilisation. In particular, the capacity of soils to catabolise different C-substrates was closely correlated (
ρ=0.604,
P=0.001) to pH. With decreasing pH, the catabolism of common low molecular weight organic compounds (especially cysteine and aspartic acid) declined, however catabolism of two others (lysine and arginine) increased. Shifts in the capacity of soil microbiota to cycle common organic compounds have implications for overall geochemical cycling of C and N in acidifying soils. The genetic structure of the bacterial communities in soil strongly correlated with pH (
ρ=0.722;
P=0.001) and that of soil fungi with pH and % sand (
ρ=0.323;
P=0.006). Catabolic function was more closely associated with the structure of the bacterial than fungal communities. This work has shown that soil pH is a primary driver of microbial diversity and function in soil. Agricultural management practices thereby act to selectively shift populations and functions against this background.
Aims
The influence of soil edaphic factors on recruitment and composition of bacteria in the legume nodule is unknown. Typically, low (acidic) pH soils have a negative effect on the plant‐rhizobia ...symbiosis and thereby reduce clover growth. However, the specific relationship between soil pH and the ecology of rhizobia is unknown, in either their free‐living or nodule‐inhabiting states. We used New Zealand pasture systems with soils of different pH, and white (WC) and subterranean (SC) clovers, to examine the relationship between soil pH and the diversity of bacteria that inhabit the nodules.
Methods and Results
Amplicon sequencing (16S rRNA) assessed the bacterial community in 5299 nodules recovered from both legume species grown in 47 soils of different edaphic (including pH) properties. Fewer nodules were formed on both clovers at low soil pH. As expected, rhizobia comprised ∼92% of the total reads in both clovers, however 28 non‐rhizobia genera were also present. Soil pH influenced the community structure of bacteria within the nodule, and this was more evident in non‐Rhizobium taxa than Rhizobium. Host strongly influenced the diversity of bacteria in the nodules. The alpha diversity of nodule microbiome in SC nodules was higher than in WC nodules and SC nodules also harbored a higher relative abundance of non‐Rhizobium bacteria than WC. Beta diversity of Rhizobium and non‐Rhizobium bacteria was influenced more by clover species rather than edaphic factors.
Conclusions
The results indicate that these clover species modified their nodule biomes in response to pH‐stress.
Significance and Impact of the Study
The non‐Rhizobium bacteria may have some functional significance (such as improved clover persistence in low pH soils) in legume nodules.
► Biogeochemistry of N in pastoral soil was examined using molecular and chemical tools. ► Urine-stimulated nitrification, denitrification and primed soil microbial communities. ► Application of ...dicyandiamide reduced formation of nitrate and nitrous oxide. ► Dicyandiamide remained effective in soil primed by previous urine application.
In pastoral farming systems, bovine urine patches are ‘hot-spots’ of elevated soil nitrogen (N). Nitrification in urine patches is linked to deleterious environmental outcomes, such as formation of the greenhouse gas nitrous oxide (N2O). The nitrification inhibitor dicyandiamide (DCD) reduces the rate of nitrification in soils subsequently limiting N-losses. Dicyandiamide's bacteriostatic mode of inhibiting ammonia oxidising bacteria (AOB), has raised concerns about the efficacy of frequent DCD use. For example, frequent use could result in selection for a DCD-tolerant AOB community. Furthermore, the impacts of DCD on other aspects of microbial N transformation in soil are largely unknown. To test the influence of short-term repeat application of DCD on soil N cycling, we established a replicated field-trial in which ±urine and ±DCD were added to pasture soils (fully crossed, 2×2 factorial design). After 57 d, treatments were re-applied. Mineral N pools, pH, DCD concentration, moisture and temperature were measured, along with N2O fluxes. Microbial communities involved in ammonia oxidation (bacteria and archaea), nitrite reduction, and N2O reduction were quantified using real-time PCR targeting functional genes (amoA, nirS, and nosZ). Overall, the addition of DCD significantly (P<0.05) reduced both the formation of nitrate (∼64%), and N2O loss from urine-treated soils (∼44%). The effect of repeating the urine and DCD applications produced similar results with no decline in DCD efficacy. This was despite a doubling in the size of the AOB community, stimulated by the initial urine application. The application of urine+DCD had a significant but minor impact on denitrifying bacteria (nirS), rather the population size of these bacteria correlated with increasing soil temperature over time (rho=0.7; P=0.002). In contrast, copies of nosZ increased with urine addition (P<0.05) but were unaffected by sampling date (increasing soil temperature). Our results demonstrate that an initial DCD application does not affect its efficacy to inhibit nitrification and reduce N2O emissions following a subsequent DCD application 57 days later.
•Trees, as long-lived, sessile, and slowly evolving organisms, are disproportionally impacted by the impacts of climate change.•Gradual and ongoing selective pressures over extended geologic ...timescales has provided co-evolutionary opportunity for both the tree and its microbiome (holobiont) to improve tree fitness under changing conditions. This co-evolution of the holobiont could infer phenological plasticity to trees to adapt to rapid climate shifts expected in the Anthropocene.•Systems-based approaches founded on complex systems sciences, holobiome theory, combined with an understanding of co-evolutionary history and application of suitable model systems will expose more opportunities to manipulate the holobiont and help us to grow climate resilient trees and forests.
Understanding the complex relationships between plants, their microbiomes, and environmental changes is crucial for improving growth and survival, especially for long-lived tree species. Trees, like other plants, maintain close associations with a multitude of microorganisms on and within their tissues, forming a 'holobiont'. However, a comprehensive framework for detailed tree-microbiome dynamics, and the implications for climate adaptation, is currently lacking. This review identifies gaps in the existing literature, emphasizing the need for more research to explore the co-evolution of the holobiont and the full extent of climate change impact on tree growth and survival. Advancing our knowledge of plant-microbial interactions presents opportunities to enhance tree adaptability and mitigate adverse impacts of climate changes on trees.
Understanding the complex relationships between plants, their microbiomes, and environmental changes is crucial for improving growth and survival, especially for long-lived tree species. Trees, like other plants, maintain close associations with a multitude of microorganisms on and within their tissues, forming a 'holobiont'. However, a comprehensive framework for detailed tree-microbiome dynamics, and the implications for climate adaptation, is currently lacking. This review identifies gaps in the existing literature, emphasizing the need for more research to explore the co-evolution of the holobiont and the full extent of climate change impact on tree growth and survival. Advancing our knowledge of plant-microbial interactions presents opportunities to enhance tree adaptability and mitigate adverse impacts of climate changes on trees.
To understand the origin of organic and condensed forms of phosphorus (P) in soils, detailed information about P forms in microorganisms is required. We isolated 7 bacteria and 8 fungi from two ...Australian soils and analyzed the P forms in their pure cultures by extraction with NaOH-EDTA followed by
31P solution nuclear magnetic (NMR) spectroscopy. The bacteria belonged to the actinobacteria and the fungi to the ascomycota, as determined by rDNA sequencing. The proportions of broad forms of P were significantly different between the bacterial and fungal isolates (analysis of similarities,
p
=
0.001). Ortho-, pyro- and polyphosphate were present in higher proportions in fungi, while monoester and diester P were present in higher proportions in bacteria. Spectral deconvolution of the monoester region revealed 15 distinct resonances. The three major ones, which were identified by spiking experiments as glycerol 1-phosphate, glycerol 2-phosphate and adenosine-5′-monophosphate (AMP), comprised 56–74% of P in the monoester region. Ordination by principal component analysis and testing for treatment effects using analysis of similarities showed significant separation of P distribution in the monoester region between bacterial and fungal isolates (
p
=
0.007). However, neither group of microorganisms had a specific single P form which might be considered characteristic. As such, it may be difficult to distinguish soil P from bacterial or fungal origins, with the possible exception of a predominantly fungal origin of pyro- and polyphosphate. The identification of three major resonances in the monoester region of microorganisms is important, since the same resonances are found in
31P NMR spectra of soil extracts.
Summary
Background
Allergic contact dermatitis (ACD) to cosmetics is widely reported. To ensure we are accurately diagnosing ACD, patch test series should be continually reviewed to identify relevant ...and emerging allergens and highlight those that are outdated. The current British Society for Cutaneous Allergy (BSCA) facial series recommends 26 allergens and was last modified in 2012.
Objectives
To review and update the BSCA facial series.
Methods
We retrospectively reviewed the results from 12 UK and Ireland patch test centres’ facial series from January 2016 to December 2017. We recorded the number of allergens tested in each centre and the detection rate for each allergen. Using a 0·3% positive rate as the inclusion threshold, we established which allergens in the BSCA facial series had positive patch test rates < 0·3% and > 0·3%. Allergens not in the BSCA facial series that had a positive patch test rate > 0·3% were identified.
Results
Overall, 4224 patients were patch tested to the facial series. The number of allergens included in individual centres’ facial series ranged from 24 to 66, with a total of 103 allergens tested across all centres. Twelve of the 26 allergens in the BSCA facial series had a positive patch test rate < 0·3% and 14 had a rate > 0·3%. Twenty‐five allergens not recommended in the BSCA facial series had a positive patch test rate > 0·3%.
Conclusions
This audit has highlighted the significant variation in practice that exists among patch test centres, despite a recommended facial series. The BSCA facial series has been updated and now contains 24 allergens. Fifteen allergens remain, 11 allergens have been dropped and nine new allergens have been added.
What is already known about this topic?
Facial dermatitis is one of the dominant presenting complaints of allergic contact dermatitis to cosmetics.
To ensure we are accurately diagnosing contact allergy, it is important that we patch test with relevant allergens.
Reviewing current literature and auditing patch test practice is a vital requirement to ensure we identify relevant and emerging allergens and highlight those that are outdated.
What does this study add?
Despite recommended patch test series, there is significant variation in practice among different patch test centres.
In response to this multicentre audit, the British Society for Cutaneous Allergy facial series has been updated and now contains 24 allergens: 15 allergens remain, 11 allergens have been dropped and nine new allergens have been added.
Linked Comment: Boonchai. Br J Dermatol 2021; 184:13.
Plain language summary available online
The microbiology within soils supports a wide range of ecosystems underpinning the productive capacity and environmental sustainability of land use. However, we have yet to make significant gains in ...the management of soil biology to achieve multiple gains across ecosystem services. Recent advances in environmental metagenomics are now enabling the characterisation of complex soil ecosystems. Advances in tools to characterise ecosystems by their DNA or RNA, alongside new approaches for the analysis of this information, are being integrated with environmental biogeochemistry to provide new insights into the functional assessment of microbial communities in relation to soil function and ecosystem services. Using these approaches, real-time assessment of drivers affecting soil phenotype (i.e. collective expression of multiple functions) can be assessed in relation to management and environmental changes, and opportunities for controlled alteration of soils for productive and environmental gains may be achieved.
Examines the extent in variation in the properties of a) variation in the population size and b) the effectiveness of N-fixation at three differentspatial scales namely: from 26 sites across New ...Zealand; at farm-wide scale; and within single fields. Source: National Library of New Zealand Te Puna Matauranga o Aotearoa, licensed by the Department of Internal Affairs for re-use under the Creative Commons Attribution 3.0 New Zealand Licence.
Tests for the impacts of land-cover type (native forest, planted forest with exotic conifers, and pastoral agriculture) on soil bacterial communities and their functional potential, using ...environmental microarrays (PhyloChip and GeoChip, respectively) across four environmentally different locations (Hokitika, Banks Peninsula, Craigieburn, and Eyrewell). Source: National Library of New Zealand Te Puna Matauranga o Aotearoa, licensed by the Department of Internal Affairs for re-use under the Creative Commons Attribution 3.0 New Zealand Licence.
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