Search

A customised synthetic microbial community (SynCom) composed of carefully selected rhizosphere-competent bacterial strains improved rice growth, yield and resistance to soil acidity and Al toxicity., (© 2024. Science China Press.)

The root-associated soil microbiome contributes immensely to support plant health and performance against abiotic and biotic stressors. Understanding the processes that shape microbial assembly in root-associated soils is of interest in microbial ecology and plant health research. In this study, 37 plant species were grown in the same soil mixture for 10 months, whereupon the root-associated soil microbiome was assessed using amplicon sequencing. From this, the contribution of direct and indirect plant effects on microbial assembly was assessed. Plant species and plant-induced changes in soil physicochemistry were the most significant factors that accounted for bacterial and fungal community variation. Considering that all plants were grown in the same starting soil mixture, our results suggest that plants, in part, shape the assembly of their root-associated soil microbiome via their effects on soil physicochemistry. With the increase in phylogenetic ranking from plant species to class, we observed declines in the degree of community variation attributed to phylogenetic origin. That is, plant-microbe associations were unique to each plant species, but the phylogenetic associations between plant species were not important. We observed a large degree of residual variation (> 65%) not accounted for by any plant-related factors, which may be attributed to random community assembly., (© The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.)

Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives. Pseudomonas bacteria were selected as a general taxonomic indicator of disease suppressive potential, while genes associated with the biosynthesis of a suite of secondary metabolites provided functional markers (GeoChip 5.0 microarray analysis). The composition of both the Pseudomonas communities and disease suppressive functional genes were responsive to land use. Underlying soil properties explained 37% of the variation in Pseudomonas community structure and up to 61% of the variation in the abundance of disease suppressive functional genes. Notably, measures of soil organic matter quality, C:P ratio, and aromaticity of the dissolved organic matter content (carbon recalcitrance), influenced both the taxonomic and functional disease suppressive potential of the pasture soils. Our results suggest that key components of the soil microbial community may be managed on-farm to enhance disease suppression and plant productivity.

Pollution induced community tolerance (PICT) to Cu(2+), and co-tolerance to nanoparticulate Cu, ionic silver (Ag(+)), and vancomycin were measured in field soils treated with Cu(2+) 15 years previously. EC50 values were determined using substrate induced respiration and correlations made against soil physicochemical properties, microbial community structure, physiological status (qCO2; metabolic quotient), and abundances of genes associated with metal and antibiotic resistance. Previous level of exposure to copper was directly (P < 0.05) associated with tolerance to addition of new Cu(2+), and also of nanoparticle Cu. However, Cu-exposed communities had no co-tolerance to Ag(+) and had increased susceptibly to vancomycin. Increased tolerance to both Cu correlated (P < 0.05) with increased metabolic quotient, potentially indicating that the community directed more energy towards cellular maintenance rather than biomass production. Neither bacterial or fungal community composition nor changes in the abundance of genes involved with metal resistance were related to PICT or co-tolerance mechanisms., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Sulphur-oxidising bacteria (SOB) play a key role in the biogeochemical cycling of sulphur in soil ecosystems. However, the ecology of SOB is poorly understood, and there is little knowledge about the taxa capable of sulphur oxidation, their distribution, habitat preferences and ecophysiology. Furthermore, as yet there are no conclusive links between SOB community size or structure and rates of sulphur oxidation. We have developed a molecular approach based on primer design targeting the soxB functional gene of nonfilamentous chemolithotrophic SOB that allows assessment of both abundance and diversity. Cloning and sequencing revealed considerable diversity of known soxB genotypes from agricultural soils and also evidence for previously undescribed taxa. In a microcosm experiment, abundance of soxB genes increased with sulphur oxidation rate in soils amended with elemental sulphur. Addition of elemental sulphur to soil had a significant effect in the soxB gene diversity, with the chemolithotrophic Thiobacillus-like Betaproteobacteria sequences dominating clone libraries 6 days after sulphur application. Using culture-independent methodology, the study provides evidence for links between abundance and diversity of SOB and sulphur oxidation. The methodology provides a new tool for investigation of the ecology and role of SOB in soil sulphur biogeochemistry., (© 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)

MicroResp™ is a miniaturised method for measuring substrate induced respiration (SIR) in soil. We modified the MicroResp™ method to develop a rapid tool for quantifying the ecotoxicological impact of contaminants. The method is based on reduction in SIR across a gradient of contaminant, allowing for determination of dose-response curves EC-values. Contaminants are mixed into soil samples at a range of concentrations; each sample is then dispensed into a column of eight wells in 96 well format (deep) plates. Moisture and glucose are added to the samples at levels to provide maximum response. Released CO₂ from the soils is then measured using colorimetric gel-traps, following the standard MicroResp™ methodology. Examination revealed that this method works over a range of soil types and is insensitive to minor variations in assay length (2-7 h), alteration of moisture content (±20 μL from optimum), and soil storage conditions (4 °C versus fresh)., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Microbial denitrification plays a key role in determining the availability of soil nitrogen (N) to plants. However, factors influencing the structure and function of denitrifier communities in the rhizosphere remain unclear. Waterlogging can result in root anoxia and increased denitrification, leading to significant N loss from soil and potential nitrous oxide (N(2)O) emissions. This study investigated denitrifier gene abundance, community structure and activity in the rhizosphere of wheat in response to anoxia and N limitation. Denitrifier community structure in the rhizosphere differed from that in bulk soil, and denitrifier gene copy numbers (nirS, nirK, nosZ) and potential denitrification activity were greater in the rhizosphere. Anoxia and N limitation, and in particular a combination of both, reduced the magnitude of this effect on gene abundance (in particular nirS) and activity, with N limitation having greater impact than waterlogging in rhizosphere soil, in contrast to bulk soil where the impact of waterlogging was greater. Increased N supply to anoxic plants improved plant health and increased rhizosphere soil pH, which resulted in enhanced reduction of N(2)O. Both anoxia and N limitation significantly influenced the structure and function of denitrifier communities in the rhizosphere, with reduced root-derived carbon postulated to play an important role., (© 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

Low-molecular-weight organic compounds in root exudates play a key role in plant-microorganism interactions by influencing the structure and function of soil microbial communities. Model exudate solutions, based on organic acids (OAs) (quinic, lactic, maleic acids) and sugars (glucose, sucrose, fructose), previously identified in the rhizosphere of Pinus radiata, were applied to soil microcosms. Root exudate compound solutions stimulated soil dehydrogenase activity and the addition of OAs increased soil pH. The structure of active bacterial communities, based on reverse-transcribed 16S rRNA gene PCR, was assessed by denaturing gradient gel electrophoresis and PhyloChip microarrays. Bacterial taxon richness was greater in all treatments than that in control soil, with a wide range of taxa (88-1043) responding positively to exudate solutions and fewer (<24) responding negatively. OAs caused significantly greater increases than sugars in the detectable richness of the soil bacterial community and larger shifts of dominant taxa. The greater response of bacteria to OAs may be due to the higher amounts of added carbon, solubilization of soil organic matter or shifts in soil pH. Our results indicate that OAs play a significant role in shaping soil bacterial communities and this may therefore have a significant impact on plant growth., (© 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

Nitrification is a key process of the nitrogen (N) cycle in soil with major environmental implications. The recent discovery of ammonia-oxidizing archaea (AOA) questions the traditional assumption of the dominant role of ammonia-oxidizing bacteria (AOB) in nitrification. We investigated AOB and AOA growth and nitrification rate in two different layers of three grassland soils treated with animal urine substrate and a nitrification inhibitor [dicyandiamide (DCD)]. We show that AOB were more abundant in the topsoils than in the subsoils, whereas AOA were more abundant in one of the subsoils. AOB grew substantially when supplied with a high dose of urine substrate, whereas AOA only grew in the Controls without the urine-N substrate. AOB growth and the amoA gene transcription activity were significantly inhibited by DCD. Nitrification rates were much higher in the topsoils than in the subsoils and were significantly related to AOB abundance, but not to AOA abundance. These results suggest that AOB and AOA prefer different soil N conditions to grow: AOB under high ammonia (NH(3)) substrate and AOA under low NH(3) substrate conditions.

The biodiversity in soil ecosystems is simultaneously incredibly rich and poorly described. In countries such as New Zealand, where high endemism in plant species emerged following extended geographical isolation, it is likely similar evolutionary pressures extended to soil microbial communities (our biodiversity 'dark matter'). However, we have little understanding of the extent of microbial life in New Zealand soils, let alone estimates of endemism, rates of species loss or gain, or implications for systems where plants and their microbiomes have co-evolved. In this study, we tested 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). This evaluation was conducted across four environmentally different locations (Hokitika, Banks Peninsula, Craigieburn, and Eyrewell). The environment from which samples were collected was the largest and most significant factor associated with variation in bacterial community assemblage and function. As such, novel pockets of bacterial biodiversity, with discrete ecosystem function, may be present in New Zealand. There was some evidence to suggest that change in land cover affected soil bacterial species, but not their functions. Secondary testing found this effect was restricted to differences between native forest and agricultural land use. Bacterial communities and functions between native and planted forests were similar. Analysis of soil environmental properties among samples found that land cover effects were underpinned by changes in soil pH that typically accompanies application of lime in agricultural systems, but is uncommon in planted forests. When compared with other studies conducted in New Zealand, we conclude that: (1) different locations can harbour distinct communities of soil microbial diversity, and (2) land-use intensification, not land cover change per se, shifts microbial biodiversity through alteration of primary habitat conditions, particularly soil pH. [ABSTRACT FROM AUTHOR]

Grasslands are an important source of biodiversity, providing a range of essential ecosystem services such as ensuring water quality and soil carbon storage. An increasing proportion of grasslands are used for pastoral agriculture, supporting production of domestic livestock. Pasture productivity is significantly affected by soil-borne microbial pathogens. Reducing the impact of soil-borne diseases in pastures is challenging given the complexity of interactions within the soil/rhizosphere microbiome and the diverse impacts of vegetation, land management, soil conditions and climate. Furthermore, there are fewer opportunities to control plant pathogens in pastures compared to arable cropping systems. The greater diversity of vegetation leads to the development of more diverse and less well characterized pathogen complexes, and the application of agrochemicals for control of soil-borne diseases is economically prohibitive and ecologically undesirable. Soil-borne plant pathogens can be suppressed through the general activity of the total soil microbiota acting in competition with the pathogenic microbiota, or by increases in the abundance and activity of specific microbes or microbial consortia that are antagonistic against selected pathogens. The development of strategies that enhance disease suppressiveness in pastures will depend not only on phylogenetic assessment of microbial communities, but also on a mechanistic understanding of the functional potential and properties (i.e. disease suppressive traits) of the soil microbiome. Collectively, this fundamental knowledge will be essential to identify the factors driving the emergence of desired disease suppressive microorganisms and traits. To understand and predict disease suppressive functionality, the spatial and temporal variability of the soil and plant-associated microbial populations and their activities must be taken into account. A systems-based approach is therefore required to identify the obstacles and opportunities related to controlling plant pathogens in pasture systems. Such an integrated approach should incorporate a “microbial” perspective to examine traits, drivers and activities of soil-borne microbes, while utilizing emerging tools in ecological genomics, as well as computational, statistical and modelling approaches that also accommodate the chemical and physical complexity of soil ecosystems. [ABSTRACT FROM AUTHOR]

Aims: Identification of soil, environmental, or microbial properties linked with efficacy of the nitrification inhibitor dicyandiamide (DCD) in high and low-input pastoral farming system soils. Methods: Soils were collected from under 25 pastures. Potential nitrification rate (PRN) was quantified in the presence and absence of DCD, and percentage efficacy of DCD in reducing PNR calculated. PNR and %DCD efficacy were statistically tested (REML analysis) for relationships to a suite of edaphic (33), environmental (5), and microbiological (8) variables. Microbiological properties included measurement of bacterial and archaeal ammonia monooxygenase genes ( amoA qPCR) and soil DNA content. Results: DCD reduced PRN by an average of 36 %. The percent DCD efficacy was not related to system intensity, soil type, nor PNR (all P > 0.05). However the numbers of bacterial amoA genes ( r = 0.46; P < 0.05), and ratios of bacterial:archaeal amoA ( r = −0.53; P < 0.05), were strongly correlated to %DCD efficacy. In both high and low input systems, models best explaining variance in %DCD efficacy fitted AOA: AOB g soil as the first varaible ( P < 0.05). Conclusions: Characterisation of soils based on ammonia oxidising communities may increase the ability to predict the % efficacy of DCD between sites and provide for more targeted application of this nitrification inhibitor. [ABSTRACT FROM AUTHOR]

Purpose: Methanotrophs are an important group of methane (CH)-oxidizing bacteria in the soil, which act as a major sink for the greenhouse gas, CH. In grazed grassland, one of the ecologically most sensitive areas is the animal urine patch soil, which is a major source of both nitrate (NO) leaching and nitrous oxide (NO) emissions. Nitrification inhibitors, such as dicyandiamide (DCD), have been used to mitigate NO leaching and NO emissions in grazed pastures. However, it is not clear if the high nitrogen loading rate in the animal urine patch soil and the use of nitrification inhibitors would have an impact on the abundance of methanotrophs in grazed grassland soils. The purpose of this study was to determine the effect of animal urine and DCD on methanotroph abundance in grazed grassland soils. Materials and methods: A laboratory incubation study was conducted to determine the effect of urine and DCD applications on the abundance of methanotrophs in six grazed grassland soils sampled from across New Zealand, using real-time PCR targeting the functional pmoA gene. Results and discussion: Results showed that the pmoA gene copy numbers were low in these soils, mostly below 2.36 × 10 g soil except in the West Coast soil where pmoA gene copy number reached 8.95 × 10 g soil. Most of the clones identified were aligned to the type II methanotrophs. There was no significant effect ( P < 0.05) on the abundance of methanotrophs by the applications of urine at 1,000 kg N ha or DCD at 10 kg ha. Conclusions: These results suggest that the abundance of methanotrophs is not affected by urine deposition or the application of DCD to mitigate NO leaching and NO emissions in grazed grassland soils. [ABSTRACT FROM AUTHOR]

Abstract: Nitrification inhibitors, such as dicyandiamide (DCD), have been shown to decrease leaching from urea- and ammonium-based fertilisers and from urine patches in grazed pastures. To date there have been few studies on effects of nitrification inhibitors on non-target soil microbiota. This pot trial examined the short-term effects of DCD on the activity and diversity of both target (ammonium-oxidising bacteria and archaea) and non-target soil microbial populations. Bovine urine at a rate equivalent to 600kgurine-Nha−1 with or without DCD at 30kgha−1 was applied to pots planted with perennial ryegrass. This rate of DCD was typical of the amount applied to pasture in New Zealand, although this annual rate may be spread over several applications carried out over 2–3 months. The single high rate application was used to provide a “worst case scenario” to assist detection of potential impacts of DCD application to non-target soil microflora. Treatments also included DCD alone and untreated control pots. Soil used was a Horotiu sandy loam and pots were maintained at 80% WHC in a controlled-environment room at 12°C/16h (day) and 8°C/8h (night). Soil mineral N, hot water extractable C and N concentrations, soil pH, microbial biomass C and N, and DCD persistence were measured at regular intervals. Diversity and composition of the overall soil bacterial community were analysed by serial analysis of ribosomal sequence tags (SARST). Effects on ammonium-oxidising bacterial and archaeal communities were monitored more closely by determining the size of these populations using real-time PCR and their transcriptional activity by comparing RNA-denaturing gradient gel electrophoresis (DGGE) profiles following RT-PCR of the amoA gene. Changes in soil pH and mineral N following application of urine in the pot trial reflected patterns typically demonstrated in the field. Application of DCD to soil did not change the diversity of the soil bacterial community, with the four predominant phyla (Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes) remaining in proportions that were similar to control soils. In contrast, urine application to soil resulted in a significant increase in members of Firmicutes, some of which are relatively stress tolerant. In line with the SARST results, shifts in the structure of the active component of the general soil bacterial community were detected in the urine and urine+DCD treatments only, further suggesting DCD had little impact on the overall soil bacterial activity. In contrast the microbes targeted by DCD, the ammonium-oxidising bacteria, were significantly affected by DCD with reductions in population size and altered activity. Ammonium-oxidising archaea, however, showed no response to application of DCD to soil, and were only minimally affected by application of urine. The results suggest that application of DCD to pasture is a relatively benign intervention that has an important role to play in mitigating the environmental hazards imposed by ongoing land use intensification. [Copyright &y& Elsevier]

New Zealand's culturally iconic, ancient kauri (Agathis australis) forests are threatened with extinction as a result of dieback caused by an invasive and highly virulent soil-borne pathogen (Phytophthora agathidicida). Kauri trees function as a foundation species in their forests, supporting an ecologically distinct plant and soil environment. The impacts of disease outbreak and subsequent tree dieback on kauri forest ecosystems, in particular soil microbial communities, remains unknown. Using high throughput amplicon sequencing and GeoChip 5 S microarray analysis we analysed the differences in diversity, taxonomic composition and functional genes related to C and N cycling of soil microbial communities associated with asymptomatic and symptomatic mature kauri. Our results found significant differences in the fungal diversity and both fungal and bacterial community composition between asymptomatic and symptomatic kauri. Several microbial taxa known in the literature for their roles in disease suppression, such as Penicillium, Trichoderma, Enterobacteriacae and Pseudomonas , were identified as being significantly higher in asymptomatic kauri soils. These findings have provided a promising direction for the discovery of disease suppressive microbial taxa against kauri dieback. In addition, the composition and abundances of microbial genes related to C and N cycling also differed significantly. These findings highlight the potential long term impacts that dieback disease may have on the health and functioning of kauri forests. • Kauri dieback disease expression alters forest soil microbial diversity and composition. • Microbial taxa related to disease suppression found higher in asymptomatic kauri soils. • Functional microbial genes related to soil C and N cycling are impacted following dieback. • Findings guide the identification of soil microorganisms which could be used as biocontrol agents against kauri dieback. [ABSTRACT FROM AUTHOR]

Abstract: Globally, tussock-based grasslands are being modified to increase productive capacity. The impacts of cultivation and over-sowing with exotic grass and legumes on soil microbiology were assessed at four sites in New Zealand which differed in soil type, climate and vegetation. Primary alteration of the soil physicochemical status occurred with land use change. This was driven by addition of mineral fertiliser and alteration of pH. Genes associated with several biogeochemical cycles (GeoChip data) were impacted by land-use but not sampling location. A number of functional gene families associated with biogeochemical cycling of C, N and S were present in greater relative abundance in the undisturbed soils. Similarly, soil bacterial (PhyloChip) and fungal (TRFLP) communities were strongly influenced by land-use change, but unaffected by sampling location. Alteration of land-use increased the relative abundance of Firmicutes, Actinobacteria and OD1 phyla, but many of the less-common phyla, such as Verrucomicrobia and Dictyoglomi decreased in abundance; these phyla may be important in internal soil nutrient cycling processes. This work provides evidence that tussock grassland soils are strongly dependent on microbially-mediated nutrient cycling, and these processes are highly-sensitive to exogenous nutrient inputs and/or alteration of pH. De-coupling of processes following addition of fertilisers or removal of organic matter (grazing) may make these improved grassland systems more susceptible to nutrient leakage. This has important implications for environmental quality. [Copyright &y& Elsevier]