Nitrogen fertilization affects bacteria utilizing plant-derived carbon in the rhizosphere of beech seedlings

Background and aims

Variation in fire intensity within an ecosystem is likely to moderate fire effects on plant and soil properties. We tested the effect of fire intensity on grassland biomass, soil microbial biomass, and soil nutrients. Additional tests determined plant-microbe, plant-nutrient, and microbe-nutrient associations.

Methods

A replicated field experiment produced a fire intensity gradient. We measured plant and soil microbial biomasses at peak plant productivity the first growing season after fire. We concurrently measured flux in 11 soil nutrients and soil moisture.

Results

Fire intensity positively affected soil nitrogen, phosphorus (P), and zinc but did not appreciably affect plant biomass, microbial biomass, and other soil nutrients. Plant biomass was seemingly (co-)limited by boron, manganese, and P. Microbial biomass was (co-)limited mainly by P and also iron.

Conclusions

In the Northern Great Plains, plant and soil microbial biomasses were limited mainly by P and some micronutrients. Fire intensity affected soil nutrients, however, pulsed P (due to fire) did not result in appreciable fire intensity effects on plant and microbial biomasses. Variable responses in plant productivity to fire are common and indicate the complexity of factors that regulate plant production after fire.

     

Soil microbial activity in relation to dissolved organic matter properties under different tree species

Background and aims

The total concentration of dissolved organic carbon (DOC) has often been observed to correlate positively with soil microbial respiration. The aim was to explain the correlation with the properties of dissolved organic matter (DOM).

Methods

A dataset from previously published papers was gathered together and subjected to multivariate analyses. Samples were collected from five tree species experiments in Finland. The degradability of DOM was assessed by measuring bacterial and fungal growth in DOM. The chemical properties of DOM were assessed by XAD resin fractionation and molecular weight. Soil microbial activity was assessed as C and N mineralization and microbial biomass.

Results

Both low and high molecular weight compounds, as well as hydrophilic neutral compounds, seemed to be relatively easily degradable. In contrast to our presupposition, easily degradable DOM seemed to be less abundant in soil where variables describing microbial activity were higher. Birch soil with higher microbial biomass N seemed to contain less easily degradable DOM than spruce soil.

Conclusion

We suggest that DOM collected and characterized at a certain point reflects more the accumulation of refractory compounds following high microbial activity than the easily degradable compounds that microbes would be using when measured.

     

Effects of phosphorus-mobilizing bacteria on tomato growth and soil microbial activity

Aims

The aim of our study was to clarify whether inoculating a soil with Pseudomonas sp. RU47 (RU47) bacteria would stimulate the enzymatic cleavage of organic P compounds in the rhizosphere and bulk soil, promoting plant growth. Adding either viable or heat treated RU47 cells made it possible to separate direct from indirect effects of the inoculum on P cycling in soil and plants.

Methods

We performed a rhizobox experiment in the greenhouse with tomato plants (Solanum lycopersicum) under low P soil conditions. Three inoculation treatments were conducted, using unselectively grown soil bacteria (bacterial mix), heat treated (HT-RU47) and viable RU47 (RU47) cells, and one not inoculated, optimally P-fertilized treatment. We verified plant growth, nutrient availability, enzyme activities and microbial community structure in soil.

Results

A plant growth promotion effect with improved P uptake was observed in both RU47 treatments. Inoculations of RU47 cells increased microbial phosphatase activity (PA) in the rhizosphere.

Conclusions

Plant growth promotion by RU47 cells is primarily associated with increased microbial PA in soil, while promotion of indigenous Pseudomonads as well as phytohormonal effects appear to be the dominant mechanisms when adding HT-RU47 cells. Thus, using RU47 offers a promising approach for more efficient P fertilization in agriculture.

     

Litter fingerprint on microbial biomass,activity, and community structure in the underlying soil

Aims

Little is known about how plant leaf litter decomposing on the soil surface is affecting microbial communities in the underlying soil. Here we examined the effects of decomposing leaf litter of different initial chemistry on biomass, stoichiometry, community structure and activity of microorganisms in the soil underneath the decaying litter layer.

Methods

Leaf litter from six different neotropical tree species with contrasted quality decomposed on top of a common tropical soil in a laboratory microcosm experiment over 98 days. At the end of the experiment we determined microbial biomass C, N, and P, microbial community structure (PLFA), and community level physiological profiles (CLPP) from the top soil.

Results

Despite growing in a common soil substrate, soil microorganisms were strongly affected by litter species, especially by the soluble litter fraction. While litters with low soluble C content did not affect the soil microbial community, litters with high soluble C content led to an increase of microbial biomass and to a structural shift to relatively more Gram-negative bacteria. Changing community structure resulted in changes of catabolic capacity of microorganisms to metabolize a range of different C substrates. The large differences in leachate N and P among litter species, in contrast, had no effect on soil microbial parameters.

Conclusions

Our data suggest that plant litter decomposing on the soil surface exhibit a strong and predictable leachate C-control over microbial community biomass, structure and function in the underlying soil.

     

Influence of diligent disintegration on anaerobic biomass and performance of microbial fuel cell

Objectives

To enhance the performance of microbial fuel cells (MFC) by increasing the surface area of cathode and diligent mechanical disintegration of anaerobic biomass.

Results

Tannery effluent and anaerobic biomass were used. The increase in surface area of the cathode resulted in 78% COD removal, with the potential, current density, power density and coulombic efficiency of 675 mV, 147 mA m^?2, 33 mW m^?2 and 3.5%, respectively. The work coupled with increased surface area of the cathode with diligent mechanical disintegration of the biomass, led to a further increase in COD removal of 82% with the potential, current density, power density and coulombic efficiency of 748 mV, 229 mA m^?2, 78 mW m^?2 and 6% respectively.

Conclusions

Mechanical disintegration of the biomass along with increased surface area of cathode enhances power generation in vertical MFC reactors using tannery effluent as fuel.

     

Maize rhizosphere priming: field estimates using <Superscript>13</Superscript>C natural abundance

Introduction

Root-mediated changes in soil organic matter (SOM) decomposition, termed rhizosphere priming effects (RPE), play crucial roles in the global carbon (C) cycle, but their mechanisms and field relevance remain ambiguous. We hypothesize that nitrogen (N) shortages may intensify SOM decomposition in the rhizosphere because of increase of fine roots and rhizodeposition.

Methods

RPE and their dependence on N-fertilization were studied using a C₃-to-C₄ vegetation change. N-fertilized and unfertilized soil cores, with and without maize, were incubated in the field for 50 days. Soil CO₂ efflux was measured, partitioned for SOM- and root-derived CO₂, and RPE was calculated. Plant biomass, microbial biomass C (MBC) and N (MBN), and enzyme activities (β-1,4-glucosidase; N-acetylglucosaminidase; L-leucine aminopeptidase) were analyzed.

Results

Roots enhanced SOM mineralization by 35 % and 126 % with and without N, respectively. This was accompanied by higher specific root-derived CO₂ in unfertilized soils. MBC, MBN and enzyme activities increased in planted soils, indicating microbial activation, causing positive RPE. N-fertilization had minor effects on MBC and MBN, but it reduced β-1,4-glucosidase and L-leucine aminopeptidase activities under maize through lower root-exudation. In contrast, N-acetylglucosaminidase activity increased with N-fertilization in planted and unplanted soils.

Conclusions

This study showed the field relevance of RPE and confirmed that, despite higher root biomass, N availability reduces RPE by lowering root and microbial activity.

     

Carry-over effects of soil inoculation on plant growth and health under sequential exposure to soil-borne diseases

Aim

To investigate the effects of biochar on biological and chemical phosphorus (P) processes and identify potential interactive effects between P fertilizer and biochar on P bioavailability in the rhizosphere of maize.

Methods

We conducted a pot-experiment with maize in a sandy loam soil with two fertilizer levels (0 and 100 mg P kg ^?1) and three biochars produced from soft wood (SW), rice husk (RH) and oil seed rape (OSR). Sequential P fractionation was performed on biochar, bulk soil, and rhizosphere soil samples. Acid and alkaline phosphatase activity and root exudates of citrate, glucose, fructose, and sucrose in the rhizosphere were determined.

Results

RH and OSR increased readily available soil P, whereas SW had no effect. However, over time available P from the biochars moved to less available P pools (Al-P and Fe-P). There were no interactive effects between P fertilizer and biochar on P bioavailability. Exudates of glucose and fructose were strongly affected by especially RH, whereas sucrose was mostly affected by P fertilizer. Alkaline phosphatase activity was positively correlated with pH, and citrate was positively correlated with readily available P.

Conclusion

Biochar effects on biological and chemical P processes in the rhizosphere are driven by biochar properties.

     

The rhizosheath – a potential trait for future agricultural sustainability occurs in orders throughout the angiosperms

Aims

Phosphorus (P) is frequently limiting crop production in agroecosystems. Large progress was achieved in understanding root traits associated with P acquisition efficiency (PAE, i.e. P uptake achieved under low P conditions). Most former studies were performed in controlled environments, and avoided the complexity of soil-root interactions. This may lead to an oversimplification of the root-soil relations. The aim of the present study was, therefore, to identify the dominant root and rhizosphere-related traits determining PAE, in contrasting soil conditions in the field.

Methods

Twenty-three maize hybrids were grown at two contrasting P levels of a long-term P-fertilizer trial in two adjacent soil types: alkaline and neutral. Bulk soil, rhizosphere and root parameters were studied in relation to plant P acquisition.

Results

Soil type had robust effect on PAE. Hybrids’ performance in one soil type was not related to that in the other soil type. In the neutral soil, roots exhibited higher specific root length, higher root/shoot ratio but lower PAE. Best performing hybrids in the neutral soil were characterized by top soil exploration, i.e., greater root surface and topsoil foraging. In contrast, in the alkaline soil, PAE and foraging traits were not correlated, P availability in the rhizosphere was greater than the bulk soil and phosphatase activity was higher, suggesting a ‘mining strategy’ in that case (i.e. traits that facilitate elevated P availability).

Conclusions

These results indicate the key role of environmental factors for roots traits determining high PAE. The study highlights the need to consider soil properties when breeding for high PAE, as various soil types are likely to require different crop ideotypes.

     

Distribution and accumulation of trace elements in rhizosphere and non-rhizosphere soils on a karst plateau after vegetation restoration

Aims

The restoration of vegetation in the rocky desertified areas of karst plateaus is a major problem for present-day ecological studies. The aim of this study was to determine the effects of vegetation restoration on the distribution and accumulation of trace elements in rhizosphere and non-rhizosphere soils.

Methods

Four representative areas containing the plants Coriaria nepalensis Wall., Pinus armandii Franch., Elaeagnus pungens Thunb., and Cotoneaster hissaricus Pojark. were selected within a vegetation restoration area in the Karst Plateau of Caohai County, Guizhou Province, China. Soils were sampled using a grid method to measure the total contents of the trace elements iron (Fe), manganese (Mn), copper (Cu), and zinc (Zn) in rhizosphere and non-rhizosphere soils.

Results

The representative area containing Elaeagnus displayed the greatest amount of accumulation in the rhizosphere of both total and available trace elements, except for total Zn. Representative areas of the rhizosphere with other types of vegetation showed accumulation of only some of the trace elements studied. All types of vegetation were associated with the bioenrichment of available trace elements in both rhizosphere and non-rhizosphere soils, except for available Cu in areas associated with Cotoneaster.

Conclusions

Representative areas containing Pinus displayed the greatest degree of bioenrichment for both total and available trace elements in both rhizosphere and non-rhizosphere soils.

     

Microbial dysbiosis and mortality during mechanical ventilation: a prospective observational study

Background

Host-associated microbial communities have important roles in tissue homeostasis and overall health. Severe perturbations can occur within these microbial communities during critical illness due to underlying diseases and clinical interventions, potentially influencing patient outcomes. We sought to profile the microbial composition of critically ill mechanically ventilated patients, and to determine whether microbial diversity is associated with illness severity and mortality.

Methods

We conducted a prospective, observational study of mechanically ventilated critically ill patients with a high incidence of pneumonia in 2 intensive care units (ICUs) in Hamilton, Canada, nested within a randomized trial for the prevention of healthcare-associated infections. The microbial profiles of specimens from 3 anatomical sites (respiratory, and upper and lower gastrointestinal tracts) were characterized using 16S ribosomal RNA gene sequencing.

Results

We collected 65 specimens from 34 ICU patients enrolled in the trial (29 endotracheal aspirates, 26 gastric aspirates and 10 stool specimens). Specimens were collected at a median time of 3?days (lower respiratory tract and gastric aspirates; interquartile range [IQR] 2–4) and 6?days (stool; IQR 4.25–6.75) following ICU admission. We observed a loss of biogeographical distinction between the lower respiratory tract and gastrointestinal tract microbiota during critical illness. Moreover, microbial diversity in the respiratory tract was inversely correlated with APACHE II score (r?=???0.46, p?=?0.013) and was associated with hospital mortality (Median Shannon index: Discharged alive; 1.964 vs. Deceased; 1.348, p?=?0.045).

Conclusions

The composition of the host-associated microbial communities is severely perturbed during critical illness. Reduced microbial diversity reflects high illness severity and is associated with mortality. Microbial diversity may be a biomarker of prognostic value in mechanically ventilated patients.

Trial registration

ClinicalTrials.gov ID NCT01782755. Registered February 4 2013.

     

Variation of soil respiration and its components in hemiboreal Norway spruce stands of different ages

Aims

Understanding the linkage of soil respiration (Rs) with forest development is essential for long-term C cycle models. We estimated the variation and temperature sensitivity (Q₁₀ value) of Rs and its hetero-, (Rh) and autotrophic (Ra) components in relation to abiotic and biotic factors in Norway spruce stands of different ages, and the effect of trenching on microbial and soil characteristics.

Methods

Trenching method was used to partition Rs into Rh and Ra. Ingrowth core method was used to estimate fine root production. Soil microbial biomass was measured using manometric respirometers.

Results

Rs varied in differently aged stands demonstrating non-linear response to development stage. The variation of Rs was explained by changes in biotic factors rather than by changes in soil microclimate. Rh was more sensitive to Ts than Rs or Ra. After 4 years of trenching soil pH, N, SOM and dehydrogenase activity were significantly changed in trenched plots compared to control plots.

Conclusions

Different Q₁₀ values of Rh and Ra in stands of different ages indicate the importance of Rs partitioning. Trenching should be used during a limited number of years because of the possible changes in chemical characteristics of soil and in the activity of soil microbial community.

     

Tree-microbial biomass competition for nutrients in a temperate deciduous forest,central Germany

Aims

Our goals were (1) to determine whether tree species diversity affects nutrient (N, P and K) cycling, and (2) to assess whether there is competition for these nutrients between microbial biomass and trees.

Methods

We measured nutrient resorption efficiency by trees, nutrient contents in leaf litterfall, decomposition rates of leaf litter, nutrient turnover in decomposing leaf litter, and plant-available nutrients in the soil in mono-species stands of beech, oak, hornbeam and lime and in mixed-species stands, each consisting of three of these species.

Results

Cycling of nutrients through leaf litter input and decomposition were influenced by the types of tree species and not simply by tree species diversity. Trees and microbial biomass were competing strongly for P, less for K and only marginally for N. Such competition was most pronounced in mono-species stands of beech and oak, which had low nutrient turnover in their slow decomposing leaf litter, and less in mono-species stands of hornbeam and lime, which had high nutrient turnover in their fast decomposing leaf litter.

Conclusions

The low soil P and K availability in beech stands, which limit the growth of beech at Hainich, Germany, were alleviated by mixing beech with hornbeam and lime. These species-specific effects on nutrient cycling and soil nutrient availability can aid forest management in improving productivity and soil fertility.

     

Carbon mineralization and microbial activity in agricultural topsoil and subsoil as regulated by root nitrogen and recalcitrant carbon concentrations

Background and aims

Biocrust morphology is often used to infer ecological function, but morphologies vary widely in pigmentation and thickness. Little is known about the links between biocrust morphology and the composition of constituent microbial community. This study aimed to examine these links using dryland crusts varying in stage and morphology.

Methods

We compared the microbial composition of three biocrust developmental stages (Early, Mid, Late) with bare soil (Bare) using high Miseq Illumina sequencing. We used standard diversity measures and network analysis to explore how microbe-microbe associations changed with biocrust stage.

Results

Biocrust richness and diversity increased with increasing stage, and there were marked differences in the microbial signatures among stages. Bare and Late stages were dominated by Alphaproteobacteria, but Cyanobacteria was the dominant phylum in Early and Mid stages. The greatest differences in microbial taxa were between Bare and Late stages. Network analysis indicated highly-connected hubs indicative of small networks.

Conclusions

Our results indicate that readily discernible biocrust features may be good indicators of microbial composition and structure. These findings are important for land managers seeking to use biocrusts as indicators of ecosystem health and function. Treating biocrusts as a single unit without considering crust stage is likely to provide misleading information on their functional roles.

     

Impacts of long-term plant biomass management on soil phosphorus under temperate grassland

Aims

We assessed and quantified the cumulative impact of 20 years of biomass management on the nature and bioavailability of soil phosphorus (P) accumulated from antecedent fertiliser inputs.

Methods

Soil (0–2.5, 2.5–5, 5–10 cm) and plant samples were taken from replicate plots in a grassland field experiment maintained for 20 years under contrasting plant biomass regimen- biomass retained or removed after mowing. Analyses included dry matter production and P uptake, root biomass, total soil carbon (C), total nitrogen (N), total P, soil P fractionation, and ³¹P NMR spectroscopy.

Results

Contemporary plant production and P uptake were over 2-fold higher for the biomass retained compared with the biomass removed regimes. Soil C, total P, soluble and labile forms of inorganic and organic soil P were significantly higher under biomass retention than removal.

Conclusions

Reserves of soluble and labile inorganic P in soil were significantly depleted in response to continued long-term removal of P in plant biomass compared to retention. However, this was only sufficient to sustain plant production at half the level observed for the biomass retention after 20 years, which was partly attributed to limited mobilisation of organic P in response to P removal.

     

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys

Background

Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis.

Results

Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion.

Conclusions

RiboTagger permits fast recovery of SSU-RNA sequences from shotgun nucleic acid surveys of complex microbial communities. The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs.

     

Interaction between contrasting rice genotypes and soil physical conditions induced by hydraulic stresses typical of alternate wetting and drying irrigation of soil

Background and aims

Drought events, agricultural practices and plant communities influence microbial and soil abiotic parameters which can feedback to fodder production. This study aimed to determine which soil legacies influence plant biomass production and nutritional quality, and its resistance and recovery to extreme weather events.

Methods

In a greenhouse experiment, soil legacy effects on Lolium perenne were examined, first under optimal conditions, and subsequently during and after drought. We used subalpine grassland soils previously cultivated for two years with grass communities of distinct functional composition, and subjected to combinations of climatic stress and simulated management.

Results

The soil legacy of climatic stress increased biomass production of Lolium perenne and its resistance and recovery to a new drought. This beneficial effect resulted from higher nutrient availability in soils previously exposed to climatic stresses due to lower competitive abilities and resistance of microbial communities to a new drought. This negative effect on microbial communities was strongest in soils from previously cut and fertilized grasslands or dominated by conservative grasses.

Conclusion

In subalpine grasslands more frequent climatic stresses could benefit fodder production in the short term, but threaten ecosystem functioning and the maintenance of traditional agricultural practices in the long term.

     

Genetic variation in the TAS2R38 taste receptor contributes to the oral microbiota in North and South European locations: a pilot study

Background

Microbial communities are influenced by environmental factors including host genetics. We investigated the relationship between host bitter taste receptor genotype hTAS2R38 and oral microbiota, together with the influence of geographical location.

Methods

hTAS2R38 polymorphisms and 16S bacterial gene sequencing from oral samples were analyzed from a total of 45 healthy volunteers from different geographical locations.

Results

Genetic variation in the bitter taste receptor TAS2R38 reflected in the microbial composition of oral mucosa in Finnish and Spanish subjects. Multivariate analysis showed significant differences in the microbial composition between country and also dependent on taste genotype. Oral microbiota was shown to be more stable to the geographical location impact among AVI-homozygotes than PAV-homozygotes or heterozygotes (PAV/AVI).

Conclusion

Geographical location and genetic variation in the hTAS2R38 taste receptor impact oral mucosa microbial composition. These findings provide an advance in the knowledge regarding the interactions between taste receptor genes and oral microbiota. This study suggests the role of host-microbiota interactions on the food taste perception in food choices, nutrition, and eating behavior.

     

Identity of plant,lichen and moss species connects with microbial abundance and soil functioning in maritime Antarctica

Background and aims

Plant breeding activities shape the rhizosphere microbiome but less is known about the relationship of both with the seed microbiome. We analyzed the composition of bacterial communities of seeds and rhizospheres of Styrian oil pumpkin genotypes in comparison to bulk soil to elucidate specific microbial signatures to support a concept involving plant-microbe interactions in breeding strategies.

Methods

The seed and rhizosphere microbiomes of 14 genotypes of oilseed pumpkin and relatives were analyzed using a 16S rRNA gene amplicon sequencing approach, which was assessed by bioinformatics and statistical methods.

Results

All analyzed microhabitats were characterized by diverse bacterial communities, but the relative proportions of phyla and the overall diversity was different. Seed microbiomes were characterized by the lowest diversity and dominant members of Enterobacteriaceae including potential pathogens (Erwinia, Pectobacterium). Potential plant-beneficial bacteria like Lysobacter, Paenibacillus and Lactococcus contributed to the microbial communities in significant abundances. Interestingly, strong genotype-specific microbiomes were detected for seeds but not for the rhizospheres.

Conclusions

Our study indicates a strong impact of the Cucurbita pepo genotype on the composition of the seed microbiome. This should be considered in breeding of new cultivars that are more capable of exploiting beneficial indigenous microbial communities.

     

Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test

Introduction

Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies.

Materials and Methods

The uptake of metabolites by microorganisms is well studied, but our knowledge of how and why they secrete different intracellular compounds is poor. The secretion of metabolites by microbial cells has traditionally been regarded as a consequence of intracellular metabolic overflow.

Conclusions

Here, we provide evidence based on time-series metabolomics data that microbial cells eliminate some metabolites in response to environmental cues, independent of metabolic overflow. Moreover, we review the different mechanisms of metabolite secretion and explore how this knowledge can benefit metabolic modeling and engineering.

     

Inter- and intra-species intercropping of barley cultivars and legume species,as affected by soil phosphorus availability

Aims

Intercropping can improve plant yields and soil phosphorus (P) use efficiency. This study compares inter- and intra-species intercropping, and determines whether P uptake and shoot biomass accumulation in intercrops are affected by soil P availability.

Methods

Four barley cultivars (Hordeum vulgare L.) and three legume species (Trifolium subterreneum, Ornithopus sativus and Medicago truncatula) were selected on the basis of their contrasting root exudation and morphological responses to P deficiency. Monocultures and barley-barley and barley-legume intercrops were grown for 6 weeks in a pot trial at very limiting, slightly limiting and excess available soil P. Above-ground biomass and shoot P were measured.

Results

Barley-legume intercrops had 10–70% greater P accumulation and 0–40% greater biomass than monocultures, with the greatest gains occurring at or below the sub-critical P requirement for barley. No benefit of barley-barley intercropping was observed. The plant combination had no significant effect on biomass and P uptake observed in intercropped treatments.

Conclusions

Barley-legume intercropping shows promise for sustainable production systems, especially at low soil P. Gains in biomass and P uptake come from inter- rather than intra-species intercropping, indicating that plant diversity resulted in decreased competition between plants for P.