Plant–microbe competition Hill, Paul W.; Jones, Davey L.
New phytologist,
01/2019, Letnik:
221, Številka:
2
Journal Article
Recenzirano
Odprti dostop
• Despite considerable attention over the last 25 yr, the importance of early protein breakdown products to plant nitrogen (N) nutrition remains uncertain.
• We used rhizosphere injection of 15N-, ...13C- and 14C-labelled inorganic N and amino acid (L-alanine), with chase periods from 1 min to 24 h, to investigate the duration of competition for amino acid between roots (Triticum aestivum) and soil microorganisms. We further investigated how microbial modification of L-alanine influenced plant carbon (C) and N recovery.
• From recovery of C isotopes, intact alanine uptake was 0.2–1.3% of added. Soil microbes appeared to remove alanine from soil solution within 1 min and release enough NH₄⁺ to account for all plant 15N recovery (over 24 h) within 5 min. Microbially generated inorganic or keto acid C accounted for < 25% of the lowest estimate of intact alanine uptake.
• Co-location of C and N labels appears a reasonable measure of intact uptake. Potential interference from microbially modified C is probably modest, but may increase with chase period. Similarly, competition for L-alanine is complete within a few minutes in soil, whereas NO₃⁻ added at the same rate is available for > 24 h, indicating that long chase periods bias outcomes and fail to accurately simulate soil processes.
Wastewater-based epidemiology (WBE) has become a complimentary surveillance tool during the SARS-CoV-2 pandemic. Viral concentration methods from wastewater are still being optimised and compared, ...whilst viral recovery under different wastewater characteristics and storage temperatures remains poorly understood. Using urban wastewater samples, we tested three viral concentration methods; polyethylene glycol precipitation (PEG), ammonium sulphate precipitation (AS), and CP select™ InnovaPrep® (IP) ultrafiltration. We found no major difference in SARS-CoV-2 and faecal indicator virus (crAssphage) recovery from wastewater samples (n = 46) using these methods, PEG slightly (albeit non-significantly), outperformed AS and IP for SARS-CoV-2 detection, as a higher genome copies per litre (gc/l) was recorded for a larger proportion of samples. Next generation sequencing of 8 paired samples revealed non-significant differences in the quality of data between AS and IP, though IP data quality was slightly better and less variable. A controlled experiment assessed the impact of wastewater suspended solids (turbidity; 0–400 NTU), surfactant load (0–200 mg/l), and storage temperature (5–20 °C) on viral recovery using the AS and IP methods. SARS-CoV-2 recoveries were >20% with AS and <10% with IP in turbid samples, whilst viral recoveries for samples with additional surfactant were between 0–18% for AS and 0–5% for IP. Turbidity and sample storage temperature combined had no significant effect on SARS-CoV-2 recovery (p > 0.05), whilst surfactant and storage temperature combined were significant negative correlates (p < 0.001 and p < 0.05, respectively). In conclusion, our results show that choice of methodology had small effect on viral recovery of SARS-CoV-2 and crAssphage in wastewater samples within this study. In contrast, sample turbidity, storage temperature, and surfactant load did affect viral recovery, highlighting the need for careful consideration of the viral concentration methodology used when working with wastewater samples.
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•Comparison of wastewater viral recovery using three concentration methods.•Control experiment looked at effect of turbidity and surfactant on viral recoveries.•No sig. difference between wastewater viral recovery methods.•Sequencing result comparable between viral concentration methods.•Solids and surfactant impact viral recovery dependant on concentration method.
The microbial partitioning of organic carbon (C) into either anabolic (i.e. growth) or catabolic (i.e. respiration) metabolic pathways represents a key process regulating the amount of added C that ...is retained in soil. The factors regulating C use efficiency (CUE) in agricultural soils, however, remain poorly understood. The aim of this study was to investigate substrate CUE from a wide range of soils (n = 970) and geographical area (200,000 km2) to determine which soil properties most influenced C retention within the microbial community. Using a 14C-labeling approach, we showed that the average CUE across all soils was 0.65 ± 0.003, but that the variation in CUE was relatively high within the sample population (CV 14.9%). Of the major properties measured in our soils, we found that pH and exchangeable aluminum (Al) were highly correlated with CUE. We identified a critical pH transition point at which CUE declined (pH 5.5). This coincided exactly with the point at which Al3+ started to become soluble. In contrast, other soil factors e.g. total C and nitrogen (N), dissolved organic C (DOC), clay content, available calcium, phosphorus (P) and sulfur (S), total base cations showed little or no relationship with CUE. We also found no evidence to suggest that nutrient stoichiometry (C:N, C:P and C:S ratios) influenced CUE in these soils. Based on current evidence, we postulate that the decline in microbial CUE at low pH and high Al reflects a greater channeling of C into energy intensive metabolic pathways involved in overcoming H+/Al3+ stress (e.g. cell repair and detoxification). The response may also be associated with shifts in microbial community structure, which are known to be tightly associated with soil pH. We conclude that maintaining agricultural soils above pH 5.5 maximizes microbial energy efficiency.
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•Microbial carbon use efficiency (CUE) was studied in 970 agricultural soils.•CUE was highly correlated with soil pH and exchangeable Al content.•A critical transition point in microbial CUE occurred at pH 5.5.•Other soil factors showed little, or no, relationship with CUE.•A decline in CUE at low pH is due to greater use of C to overcome acid stress.
We investigated how the legacy of warming and summer drought affected microbial communities in five different replicated long‐term (>10 years) field experiments across Europe (EU‐FP7 INCREASE ...infrastructure). To focus explicitly on legacy effects (i.e., indirect rather than direct effects of the environmental factors), we measured microbial variables under the same moisture and temperature in a brief screening, and following a pre‐incubation at stable conditions. Specifically, we investigated the size and composition of the soil microbial community (PLFA) alongside measurements of bacterial (leucine incorporation) and fungal (acetate in ergosterol incorporation) growth rates, previously shown to be highly responsive to changes in environmental factors, and microbial respiration. We found no legacy effects on the microbial community size, composition, growth rates, or basal respiration rates at the effect sizes used in our experimental setup (0.6 °C, about 30% precipitation reduction). Our findings support previous reports from single short‐term ecosystem studies thereby providing a clear evidence base to allow long‐term, broad‐scale generalizations to be made. The implication of our study is that warming and summer drought will not result in legacy effects on the microbial community and their processes within the effect sizes here studied. While legacy effects on microbial processes during perturbation cycles, such as drying–rewetting, and on tolerance to drought and warming remain to be studied, our results suggest that any effects on overall ecosystem processes will be rather limited. Thus, the legacies of warming and drought should not be prioritized factors to consider when modeling contemporary rates of biogeochemical processes in soil.
The factors regulating potential acquisition of sulphur (S)-containing amino acids by plant roots from the rhizosphere remain poorly understood. Using radio tracer (
14
C and
35
S), we studied the ...competition for two S-containing amino acids (i.e., cysteine (Cys) and methionine (Met)) within 24 hours (h), by the rhizosphere microbial community and maize plants (
Zea mays
L.). Our results showed that the capture of Cys and Met by the maize plants was much lower, with only <10% of the added amino acid-
14
C or
35
S captured by the plant, compared to the rhizosphere microbial community (76.9%) on average. We suggest that this could be a result of relatively high availability of inorganic N and S in soil solution, the lack of transmembrane for amino acids on maize root cells, as well as the rapid turnover of Cys and Met by soil microbes in the rhizosphere. The addition of inorganic S, significantly reduced plant capture of Cys and Met-
14
C by maize plants in the rhizosphere but had little effect on the capture of Cys and Met-
35
S (
p
<0.05). Overall, our results imply that (1) Cys and Met are available carbon (C), nitrogen (N) and S sources for maize plants, potentially contributing to total plant N and S demand under certain conditions; (2) Utilization of Cys and Met by maize roots in the rhizosphere is independent of inorganic S availability; (3) Increased amino acid concentration led to higher capture by both plants and soil microbes, but had little effect on the competition success on either side.
The impacts of neonicotinoids have generally focussed on the responses of the pure active ingredient. Using a selection of two commercial formulations and the active ingredient, we ran three ...laboratory studies using 14C-labelled acetamiprid to study the leaching, sorption and mineralisation behaviours of the commercially available neonicotinoid formulations compared to the pure active ingredient. We added 14C-spiked acetamiprid to a sandy loam soil that had received long-term additions of farmyard manure at two rates (10 t/ha/yr and 25 t/ha/yr) and mineral fertilisers, as a control. We found significant differences in acetamiprid mineralisation across both the SOM and chemical treatments. Sorption was primarily impacted by changes in SOM and any differences in leachate recovery were much less significant across both treatment types. The mineralisation of all pesticide formulations was comparatively slow, with <23 % of any given chemical/soil organic matter combination being mineralised over the experimental period. The highest mineralisation rates occurred in samples with the highest soil organic matter levels. The results also showed that 82.9 % ± 1.6 % of the acetamiprid applied was leached from the soil during repeated simulated rainfall events. This combined with the low sorption values, and the low rates of mineralisation, implies that acetamiprid is highly persistent and mobile within sandy soils. As a highly persistent neurotoxin with high invertebrate selectivity, the presence of neonicotinoids in soil presents a high toxicology risk to various beneficial soil organisms, including earthworms, as well as being at high risk of transfer to surrounding watercourses.
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•The mineralisation, sorption and leaching of 3 acetamiprid products were tested.•Pure acetamiprid behaved similar to the commercial formulations.•Increases in soil organic matter can decrease the availability of acetamiprid in soil.•Acetamiprid does not sorb strongly to the solid phase and is mobile in soil.•High mobility of soil applied-acetamiprid poses a risk to the wider environment.
Rhizodeposits have received considerable attention, as they play an important role in the regulation of soil carbon (C) sequestration and global C cycling and represent an important C and energy ...source for soil microorganisms. However, the utilization of rhizodeposits by microbial groups, their role in the turnover of soil organic matter (SOM) pools in rice paddies, and the effects of nitrogen (N) fertilization on rhizodeposition are nearly unknown. Rice (
Oryza sativa
L.) plants were grown in soil at five N fertilization rates (0, 10, 20, 40, or 60 mg N kg
−1
soil) and continuously labeled in a
13
CO
2
atmosphere for 18 days during tillering. The utilization of root-derived C by microbial groups was assessed by
13
C incorporation into phospholipid fatty acids. Rice shoot and root biomass strongly increased with N fertilization. Rhizodeposition increased with N fertilization, whereas the total
13
C incorporation into microorganisms, as indicated by the percentage of
13
C recovered in microbial biomass, decreased. The contribution of root-derived
13
C to SOM formation increased with root biomass. The ratio of
13
C in soil pools (SOM and microbial biomass) to
13
C in roots decreased with N fertilization showing less incorporation and faster turnover with N. The
13
C incorporation into fungi (18:2ω6,9c and 18:1ω9c), arbuscular mycorrhizal fungi (16:1ω5c), and actinomycetes (10Me 16:0 and 10Me 18:0) increased with N fertilization, whereas the
13
C incorporation into gram-positive (i14:0, i15:0, a15:0, i16:0, i17:0, and a17:0) and gram-negative (16:1ω7c, 18:1ω7c, cy17:0, and cy19:0) bacteria decreased with N fertilization. Thus, the uptake and microbial processing of root-derived C was affected by N availability in soil. Compared with the unfertilized soil, the contribution of rhizodeposits to SOM and microorganisms increased at low to intermediate N fertilization rates but decreased at the maximum N input. We conclude that belowground C allocation and rhizodeposition by rice, microbial utilization of rhizodeposited C, and its stabilization within SOM pools are strongly affected by N availability: N fertilization adequate to the plant demand increases C incorporation in all these polls, but excessive N fertilization has negative effects not only on environmental pollution but also on C sequestration in soil.
Objectives: Afforestation changes soil chemical properties over several decades. In contrast, microbial community structure can be shifted within the first decade and so, the direct effects of tree ...species can be revealed. The aim of this study was to determine the alteration of soil microbial community composition 10 years after afforestation by trees with contrasting functional traits. Methods: The study was conducted at the BangorDIVERSE temperate forest experiment. Soil samples were collected under single, two and three species mixtures of alder and birch, beech and oak - early and secondary successional species, respectively, and contiguous agricultural field. Soil was analysed for total carbon (C) and nitrogen (N) contents, and microbial community structure (phospholipid fatty acids (PLFAs) analysis). Results and conclusions: The total PLFAs content (370-640 nmol g⁻¹ soil) in forest plots increased for 30 to 110 % compared to the agricultural soil (290 nmol g⁻¹ soil). In contrast, soil C, N and C/N ratios were altered over 10 years much less - increased only up to 20 % or even decreased (for beech forest). Afforestation increased bacterial PLFAs by 20-120 %, whereas it had stronger impact on the development of fungal communities (increased by 50-200 %). These effects were proved for all forests, but were more pronounced under the monocultures compared to mixtures. This indicates that species identity has a stronger effect than species diversity. Principal component analysis of PLFAs revealed that under mono and three species mixtures similar microbial communities were formed. In contrast, gram-positive PLFAs and actinomycete PLFAs contributed mainly to differentiation of two species mixtures from other forests. Thus, at the early afforestation stage: i) soil biological properties are altered more than chemical, and ii) tree species identity affects more than species amount on both processes.
The process of nitrogen (N) transformation after microbial utilisation of organic and inorganic N is unclear.
15
N
-glycine (Gly),
15
NH
4
+
and
15
NO
3
−
were used to investigate the uptake, release ...and reutilisation of N by microorganisms over 9 days. In addition, high amounts of unlabelled carbon (C) or N were added to explore how C or N availability affects the cycling of inorganic and organic N by microorganisms. Within 15 min, 67% of the added
15
N-Gly was taken up by soil microorganisms; within 1 h, 8% was released as NH
4
+
. The released
15
NH
4
+
was reutilised by the microorganisms within hours. Microorganisms took up 50% of the added
15
NH
4
+
(15 min) and released 13% of the taken up NH
4
+
(1 h). Microorganisms prefer to take up Gly rather than NH
4
+
because they can directly acquire C from Gly for maintaining its growth and synthesising more complex compounds. NO
3
−
was taken up by microorganisms within minutes but not released into the soil. NO
3
−
was likely stored in the cytoplasm, to be used as an N source to face future N-deficient environments. When high concentrations of C or N were added, the assimilation of Gly and NH
4
+
increased, whereas N mineralisation and nitrification rates decreased, and the uptake of NO
3
−
remained stable. Overall, Gly and NH
4
+
were taken up, released and re-taken up by microorganisms and were preferentially utilised under excess C or N sources, while NO
3
−
was stored in the microbiome. These findings provide new insights into N uptake by microorganisms in short-term.
High levels of heavy metals in soil can ultimately lead to pollution of drinking water and contamination of food. Consequently, sustainable remediation strategies for treating soil are required. The ...potential ameliorative effect of several composts derived from source-separated and mixed municipal wastes were evaluated in a highly acidic heavily contaminated soil (As, Cu, Pb, Zn) in the presence and absence of lime. Overall, PTE (potentially toxic element) amelioration was enhanced by compost whilst lime had little effect and even exacerbated PTE mobilization (e.g. As). All composts reduced soil solution PTE levels and raised soil pH and nutrient levels and are well suited to revegetation of contaminated sites. However, care must be taken to ensure correct pH management (pH 5–6) to optimize plant growth whilst minimizing PTE solubilization, particularly at high pH. In addition, ‘metal excluder’ species should be sown to minimize PTE entry into the food chain.
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