Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition

Plant roots select non‐random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonized by different fungi and analyzed differences in microbiome structure related to soils from distinct podzol horizons and effects of short‐term additions of N, a growth‐limiting nutrient commonly applied as a fertilizer, but known to influence patterns of carbon allocation to roots. Ectomycorrhizal roots growing in soil from different horizons harboured distinct bacterial communities. The fungi colonizing individual roots had a strong effect on the associated bacterial communities. Even closely related species within the same ectomycorrhizal genus had distinct bacterial microbiomes in unfertilized soil, but fertilization removed this specificity. Effects of N were rapid and context dependent, being influenced by both soil type and the particular ectomycorrhizal fungi involved. Fungal community composition changed in soil from all horizons, but bacteria only responded strongly to N in soil from the B horizon where community structure was different and bacterial diversity was significantly reduced, possibly reflecting changed carbon allocation patterns.     

Depth-Related Changes in Community Structure of Culturable Mineral Weathering Bacteria and in Weathering Patterns Caused by Them along Two Contrasting Soil Profiles

Bacteria play important roles in mineral weathering and soil formation. However, few reports of mineral weathering bacteria inhabiting subsurfaces of soil profiles have been published, raising the question of whether the subsurface weathering bacteria are fundamentally distinct from those in surface communities. To address this question, we isolated and characterized mineral weathering bacteria from two contrasting soil profiles with respect to their role in the weathering pattern evolution, their place in the community structure, and their depth-related changes in these two soil profiles. The effectiveness and pattern of bacterial mineral weathering were different in the two profiles and among the horizons within the respective profiles. The abundance of highly effective mineral weathering bacteria in the Changshu profile was significantly greater in the deepest horizon than in the upper horizons, whereas in the Yanting profile it was significantly greater in the upper horizons than in the deeper horizons. Most of the mineral weathering bacteria from the upper horizons of the Changshu profile and from the deeper horizons of the Yanting profile significantly acidified the culture media in the mineral weathering process. The proportion of siderophore-producing bacteria in the Changshu profile was similar in all horizons except in the Bg2 horizon, whereas the proportion of siderophore-producing bacteria in the Yanting profile was higher in the upper horizons than in the deeper horizons. Both profiles existed in different highly depth-specific culturable mineral weathering community structures. The depth-related changes in culturable weathering communities were primarily attributable to minor bacterial groups rather than to a change in the major population structure.     

Influence of dolomitic lime on DOC and DON leaching in a forest soil

The influence of liming on leaching and distribution of dissolved organic carbon (DOC) and nitrogen (DON) in mineral soil was investigated in a leaching experiment with soil columns. Soil samples from separate horizons (O, A and B horizons) were collected from control and limed plots in a field liming experiment in a spruce forest in southern Sweden. The field liming (0.88 kg m^-2) had been carried out 8 years before sampling. To minimize the variation among replicates, soil profiles were reconstructed in the laboratory so that the dry weight was the same for each individual soil horizon regardless of treatment. Two soil column types were used with either the O+A horizons or the O+A+B horizons. One Norway spruce seedling (Picea abies (L.) Karst) was planted in each soil column. Average pH in the leachate water was greater in the limed treatment than in the control treatment (5.0 versus 4.0 for O+A columns and 4.3 versus 3.8 for O+A+B columns). After reaching an approximate steady state, the leaching of DOC was 3--4 times greater from the limed O+A and O+A+B columns than from the corresponding control columns but the leaching of DON increased (3.5 times) only in the limed O+A columns. There was a significant correlation between DOC and DON in the leachates from all columns except for the control O+A+B columns, which indicated a decoupling of DOC and DON retention in the B horizon in the control treatment. This might be explained by a selective adsorption of nitrogen poor hydrophobic compounds (C/N ratio: 32--77) while there was a lower retention of nitrogen rich hydrophilic compounds (C/N ratio: 14--20). Proportionally more hydrophobic compounds were leached from the limed soil compared to the unlimed soil. These hydrophobic compounds also became more enriched in nitrogen after liming so in the limed treatment nitrogen might be adsorbed at nearly the same proportion as carbon, which might explain the fact that there was no decoupling of leached DOC and DON from the B horizon after liming.     

Bacterial and fungal communities in bulk soil and rhizospheres of aluminum-tolerant and aluminum-sensitive maize (Zea mays L.) lines cultivated in unlimed and limed Cerrado soil

Liming of acidic soils can prevent aluminum toxicity and improve crop production. Some maize lines show aluminum (Al) tolerance, and exudation of organic acids by roots has been considered to represent an important mechanism involved in the tolerance. However, there is no information about the impact of liming on the structures of bacterial and fungal communities in Cerrado soil, nor if there are differences between the microbial communities from the rhizospheres of Al-tolerant and Al-sensitive maize lines. This study evaluated the effects of liming on the structure of bacterial and fungal communities in bulk soil and rhizospheres of Al-sensitive and Al-tolerant maize (Zea mays L.) lines cultivated in Cerrado soil by PCR-DGGE, 30 and 90 days after sowing. Bacterial fingerprints revealed that the bacterial communities from rhizospheres were more affected by aluminum stress in soil than by the maize line (Al-sensitive or Al-tolerant). Differences in bacterial communities were also observed over time (30 and 90 days after sowing), and these occurred mainly in the Actinobacteria. Conversely, fungal communities from the rhizosphere were weakly affected either by liming or by the rhizosphere, as observed from the DGGE profiles. Furthermore, only a few differences were observed in the DGGE profiles of the fungal populations during plant development when compared with bacterial communities. Cloning and sequencing of 16S rRNA gene fragments obtained from dominant DGGE bands detected in the bacterial profiles of the Cerrado bulk soil revealed that Actinomycetales and Rhizobiales were among the dominant ribotypes.     

Characterization of Depth-Related Changes in Bacterial Communities Involved in Mineral Weathering Along a Mineral-Rich Soil Profile

In this study, we used denaturing gradient gel electrophoresis (DGGE) and culture-dependent methodology to characterize bacterial populations and mineral-dissolving bacteria in a mineral-rich soil profile. DGGE and sequencing revealed 13 known bacterial families and 7 unknown populations for the soil profile. Seventy-one isolates could solubilize feldspar. Weathering effectiveness and pattern of the isolates differed among the horizons. The 71 mineral-dissolving isolates were affiliated with 32 bacterial species within 14 genera, among which Bacillus, Burkholderia, and Arthrobacter were dominant. Distinct mineral-dissolving populations were observed between the surface and subsurface horizons. Notably, the deepest horizon showed maximum diversity of the mineral-dissolving bacteria. Furthermore, a significantly higher proportion of the high efficiency mineral-dissolving bacteria was observed in the deeper horizons than in the upper horizons. The results suggested that the soil profile harboured diverse mineral-dissolving populations and the dissolving potential and pattern and the community of the mineral-dissolving bacteria changed with depth.     

不同重金属污染水平下生物结皮及下层土壤细菌群落的差异性分析

为了探究生物结皮及下层土壤细菌群落多样性及结构在不同重金属污染水平下的差异及其影响因素,以宁夏东部工矿区和封育草地内广泛分布的两类生物结皮为研究对象,采用高通量测序技术,分析结皮层(A层)和结皮下层(B层)土壤细菌群落结构和多样性差异。采用相关分析、冗余分析探讨两个生境生物结皮各层次细菌群落与土壤环境因子的关系。结果表明：(1)相较于封育区,工矿区2类生物结皮对源自大气降尘的重金属元素具有更显著的表层富集作用,并表现出显著的种间差异：苔藓结皮>藻结皮。污染负荷指数评价结果显示：工矿区生物结皮各层次重金属污染程度更高,且均表现为A层污染程度高于B层。(2)两个生境的优势细菌门组成基本一致,均为放线菌门、变形菌门、酸杆菌门。受生物结皮类型、重金属污染程度的影响,细菌群落结构差异显著,主要表现为：工矿区藻结皮A、B层的α多样性指数均大于封育区,而苔藓结皮A、B层的细菌多样性指数高于封育区,丰富度指数低于封育区。主坐标分析结果显示,不同生境的生物结皮细菌群落结构差异明显,而同一生境的生物结皮细菌群落结构相似。重金属As、Pb、土壤黏粒含量和pH是影响生物结皮细菌群落结构的主要土壤环境因子...     

Factors controlling spatial distribution of soil acidification and Al forms in forest soils

Soil acidification and Al release in forest soils is controlled by a number of factors, like acid deposition, forest type, parent rock, altitude, etc. This paper studies the principal stand factors affecting spatial distribution of the content of KCl-extractable Al (Al(KCl), mainly exchangeable), Na4P2O7-extractable Al (Al(Na4P2O7), mainly organically bound), and other soil characteristics related to acidification in surface organic (O) and subsurface mineral (B) horizons in the Jizera Mountains region. Geostatistical methods were exploited. The highest Al(KCl) contents in the O horizons were related to high S and N content, low pH and low Ca and Mg content in soil. Liming decreased Al(KCl) contents in the O horizons. Al(Na4P2O7) in the O horizons was more abundant under spruce than under beech; in both horizons it was increased on the immission clear-cut areas populated by grass. Surface horizons are more sensitive to external influence (acid deposition, liming) and their spatial variation is stronger. In the mineral horizons, the effect of pedogenetic processes is more important. The effect of stand factors on Al behaviour is complex and often indirect, mediated for example by organic matter or soil reaction. It is difficult to clearly distinguish the effects of the particular factors.     

A novel method for sampling bacteria on plant root and soil surfaces at the microhabitat scale

This study reports the first method for sampling bacteria at a spatial scale approximating a microhabitat. At the core of this method is the use of tungsten rods with laser-cut tips of known surface area (0.013 mm(2)). Exposed plant root or soil surfaces were viewed with a dissecting microscope and micro-sampling rods were guided to sample sites using a micro-manipulator. Bacteria that adhered to the sampling tips were then recovered for microbiological analyses. The efficiency of this method for removing bacteria from root surfaces was similar to that with which bacteria are recovered from dissected root segments using the conventional technique of washing. However, as the surface area of the micro-sampling tips was known, the new method has the advantage of eliminating inaccuracy in estimates of bacterial densities due to inaccurate estimation of the root or soil surface sampled. When used to investigate spatial distributions of rhizoplane bacteria, the new technique revealed trends that were consistent with those reported with existing methods, while providing access to additional information about community structure at a much smaller spatial scale. The spatial scale of this new method is ca. 1000-times smaller than other sampling methods involving swabbing. This novel technique represents an important methodological step facilitating microbial ecological investigations at a microhabitat scale.     

Influence of soil thickness on stand characteristics in a Sierra Nevada mixed-conifer forest

Soil thickness can be an important factor influencing vegetation, yet few spatially-explicit studies have examined soil horizon thickness and vegetation composition in summer-drought forests. We compared seismic and soil penetration measurements of combined A + C and Cr horizon thickness, soil moisture and temperature, and stand variables in a contiguous 4-ha mixed-conifer stand of the Sierra Nevada. Thickness of A + C and Cr horizons were highly variable but were not correlated to each other. Total basal area and canopy cover were positively related with A + C horizon thickness, and shrub cover was positively related with Cr horizon thickness. Basal area of white fir [Abies concolor (Gord and Glend) Lindl.] and incense-cedar [Calocedrus decurrens (Torrey) Florin] were positively correlated with A + C horizon thickness, but there was no relationship between A + C or Cr horizon thickness and basal area of Jeffrey pine (Pinus jeffreyi Grev. and Balf.), sugar pine (P. lambertiana Douglas), or red fir (A. magnifica A. Murray). Both white and red fir seedlings were associated with decreased soil temperature, but only white fir seedlings were positively associated with soil moisture. Soil penetration estimates of soil thickness were similar to seismic estimates for shallow soils (<50 cm depth) but were poorly related on deeper soils. Visual surface conditions and tile probe estimates of soil thickness can be highly misleading because ‘shallow’ areas may have a thick layer of weathered bedrock that can serve as a potential rooting medium for deep-rooted trees and shrubs. In our study only the refraction seismic method had the potential to measure total soil depth that included A + C and Cr horizon thickness.     

Effects of watershed liming on the soil chemistry of Woods Lake,New York

The effects of watershed liming on the exchange complex of a forest soil were investigated at Woods Lake, in the west-central Adirondack Park, New York. Attempts to neutralize lake acidity via direct application of calcite during the 1980"s were short-lived due to a short hydraulic retention time. The Experimental Watershed Liming Study (EWLS) was initiated to investigate watershed base addition as a potentially more long-term strategy for mitigation of lake acidity. In this paper we discuss the changes in the exchangeable soil complex which occurred in response to the calcite addition and attempt a mass balance for calcite applied to the watershed.An extensive sampling program was initiated for the watershed study. Soil samples were collected from pits prior to and in the two years following treatment to evaluate changes in soil chemistry. Calcite addition significantly altered the exchange complex in the organic horizon. Increases in pH caused deprotonation of soil organic matter and increases in cation exchange capacity, providing additional exchange sites for the retention of added calcium. Exchangeable acidity decreased to very low values, allowing the base saturation of upper organic horizons to increase to nearly 100 percent.Post-treatment sampling found that approximately 48 percent of the calcite remained undissolved in the soil"s Oe horizon two years later. Dissolution of the calcite was affected by field moisture conditions, with greater dissolution in wetter areas of the watershed. Mass balances calculated for calcium applied to the watershed suggest that only 4 percent of the calcium was removed through the lake outlet. Approximately 96 percent of the calcium applied remained within the watershed; as undissolved calcite, on soil exchange sites or stored in the vegetation, groundwater or surface waters of the watershed.     

Linkage Between Culturable Mineral-Weathering Bacteria and their Weathering Effectiveness Along a Soil Profile

In this study, we used culture-dependent methodology to characterize the weathering effectiveness and community of culturable mineral-weathering bacteria in an ultisol profile. A total of 261 isolates were obtained and found to have the ability to weather biotite. The proportions of the highly effective Si and Al solubilizers were significantly higher in the D and E horizons than in the A, B, C, and F horizons, while the A, B, C, and F horizons had the similar proportion of the highly effective Si solubilizers. The B and F horizons had the lowest proportion of the highly effective Al solubilizers. The D horizon had the maximum proportion of the highly effective Fe solubilizers. Lowest proportion of the highly effective Fe solubilizers was observed in the A and F horizons. The 261 mineral-weathering isolates were affiliated with 39 bacterial species within 19 genera. Burkholderia anthina from the A and B horizons, Burkholderia stabilis from the C, D, and E horizons, and Curtobacterium citreum from the F horizon had the significantly higher ability to release Si, Al, and Fe from biotite. The results showed the diverse mineral-weathering bacteria and the linkage between the weathering species and their weathering effectiveness along a soil profile.     

Effect of cell density and attachment on resuscitation in soil of starved Pseudomonas fluorescens MON787

The effect of cell density and attachment on starvation survival and recovery was determined using luminometry to measure activity of a lux -marked strain of Pseudomonas fluorescens MON787. Bioluminescence was found to be a sensitive indicator of in situ activity of P. fluorescens MON787 in soil. The activity of a bacterial inoculum could be monitored during growth in soil, and was found to correlate with an increase in cell numbers. Luminescence could detect decreasing activity of P. fluorescens during starvation in soil, and recovery of activity and cell numbers following exposure to starvation and matric potential stress. The effect of localised cell density and attachment in soil on recovery from lag phase after nutrient addition was investigated and compared to recovery of starved liquid cultures. Nutrient addition to starved P. fluorescens in soil or liquid medium resulted in an immediate recovery of activity, followed by a second increase in luminescence after 5 h. Cells exposed to both starvation and matric potential stress in soil did not show a detectable immediate increase of activity, but required a 5-h lag phase before recovery of both activity and cell growth. The lag phase values were not significantly different over a range of localised cell densities. This suggests that cell density of P. fluorescens in the range tested is not a factor which affects recovery of soil bacteria from starvation.     

Ectomycorrhizal exudates and pre-exposure to elevated CO2 affects soil bacterial growth and community structure

Ectomycorrhizal fungi produce low molecular weight organic compounds, supporting diverse microbial communities. To link mycorrhizal root exudation directly to bacterial responses, we used Scots pine exudates with (Suillus variegatus and Piloderma fallax) and without mycorrhiza as substrata for forest soil bacteria. Bacterial growth and vitality was monitored, and community composition determined using T-RFLP, cloning and sequencing. We investigated if the amount of organic acids in exudates explained bacterial growth, and whether bacterial communities were influenced by pre-exposure to elevated atmospheric CO₂. We demonstrated functional differences in bacterial growth rates related to CO₂. There was a shift in the bacterial community (e.g. Burkholderia sp. and gamma-proteobacteria) toward organisms better able to rapidly utilize exudates when pine microcosms were pre-exposed to elevated CO₂. Soil bacteria from all treatments tended to grow more abundantly and rapidly in exudates from Piloderma-colonized seedlings, suggesting that the organic acids and/or unidentified compounds present supported greater growth.     

Regulation of Fusarium oxysporum population introduced into soil: the amoebal predation hypothesis

Abstract Inoculation of fungi into soil has been suggested for biological control of plant diseases. The aim of our work was to test the ability of protozoa to reduce the density of introduced fungal populations. The survival of Fusarium oxysporum in non-sterile soil was studied after introduction at densities of: 1 × 10⁴, 1 × 10⁶ and 5 × 10⁷ cfu/g soil. The dynamics of protozoa were also followed. The fungal populations remained close to the initial inoculation densities and did not induce the growth of indigenous protozoa. A bacterial population ( Enterobacter aerogenes ) was used to promote and stimulate the predatory activity of amoebae. Then, after simultaneous inoculation with bacteria and fungi, the density of protozoa increased but this had no effect on the fungal population, although some amoebae are able to feed on small fungal propagules such as conidia. The physiological state of Fusarium in soil and intraspecific competition seem to be more important in regulating introduced fungal populations than amoebal predation. We conclude that the regulation of bacterial and fungal populations in soil depend on different mechanisms.     

Vertical root distribution in relation to soil properties in New Jersey Pinelands forests

Vertical distribution of root density (length per unit soil volume) and abundance (length per unit ground surface area) to a depth of 1.5 m or to the depth of the water table and their relationships with soil properties and tree basal area were examined in 36 soil profiles of pine-oak and oak-pine forests of the New Jersey Pinelands. Soil morphology were almost uniform within the forest type and characterized by the presence of high coarse fragment contents in the C horizon in oak-pine uplands; by the spodic B horizon and water table in the C horizon in pine-oak lowlands; by the sandy soil throughout the profile in pine-oak uplands; and by the firm argillic B horizon in pine-oak plains. Root density decreased from ranges of 44423–133369 m m^-3 in the 0–5 cm depth in all the forest types to 1900–5593 m m^-3 in the 100–150 cm depth in all the forest types except in pine-oak lowlands. Total profile root density and abundance was in the order: oak-pine uplands>pine-oak lowlands>pine-oak uplands>pine-oak plains. Root density correlated positively with organic C, total N, water soluble P, exchangeable Ca, Mg, K, Al, Fe, and cation exchange capacity, and negatively with bulk density, coarse fraction content, and pH, whereas root abundance correlated positively with organic C, total N, water soluble P, exchangeable Ca, Mg, K, and Fe, and negatively with bulk density. No correlation existed between root density and abundance with tree basal area. Higher root density in the E horizon of oak-pine uplands as compared to the other forest types was associated with high nutrient content; higher root density in the C horizon of pine-oak lowlands was associated with a shallow water table beneath the horizon; and lower root densities in the B and C horizons of pine-oak plains were associated with the presence of a firm clay layer in the B horizon.     

Long-term effects of grassland management on soil microbial abundance: implications for soil carbon and nitrogen storage

Grassland management intensification can significantly affect the structure and composition of important soil microbial groups such as bacteria and fungi. Changes to these microbial communities can greatly influence carbon (C) and nitrogen (N) cycling in grassland soils. Here we specifically address how microbial abundances might shift under the effect of multiple management practices and how this in turn might relate to changes in soil C and N storage. Soil samples were collected from a 23-year-old grassland experiment and real-time quantitative Polymerase Chain Reaction (PCR) was performed to address whether and how (1) chronic nutrient additions, (2) liming (i.e., the addition of CaCO₃ to soils), and (3) grazing by rabbits might affect archaeal, bacterial and fungal microbial groups. We found that liming additions significantly increased archaeal and bacterial abundance whilst strongly reducing fungal abundance. The addition of N-only (as NH₄NO₃) significantly reduced bacterial abundance while chronic grazing by rabbits resulted in positive effects on archaeal abundance. Despite long-term grassland management significantly affecting soil microbial abundances (and Fungal-to-Bacterial ratios), microbial changes were not related to either changes in soil C or N pools. Overall, our results suggest that (1) important microbial-‘soil functioning’ relationships may only be detected at lower taxonomic levels, and (2) liming-induced increases in soil pH determined significant shifts in soil microbial abundance, which could have important consequences for the delivery of multiple soil ecosystem services (i.e., nutrient regulation, C and N sequestration) from permanent grassland.     

盐度对滨海土壤细菌多样性和群落构建过程的影响

滨海盐土是重要的农业土地后备资源。微生物是土壤中物质循环的关键动力,然而盐度对土壤微生物群落特征影响的研究还很缺乏。本研究采集滨海地区的土壤样品,研究非盐、轻盐和高盐3组不同盐度对土壤细菌数量、多样性和群落构建的影响。结果表明: 与非盐和轻盐土壤相比,高盐土壤的脱氢酶活性和细菌数量显著降低,而细菌α多样性没有变化,细菌群落结构发生分异。利用零模型反演群落构建过程,发现盐度是细菌群落构建过程的主控因子,盐度主导的高确定性过程控制了滨海盐土细菌的群落结构。说明在现有的盐度范围内,高盐土壤中同样含有丰富的微生物种质资源,具有盐土改良的生物学基础,然而由于高确定性的群落构建机制,外源物种很难定殖于滨海盐土。因此,在利用微生物技术改良滨海盐土时,应尽可能筛选耐盐的土著菌种,提高定殖效率。     

Influence of soil pH on the nitrate-reducing microbial populations and their potential to reduce nitrate to NO and N2O

Abstract After the introduction of Rhizobium leguminosarum biovar trifolii into natural loamy sand and silt loam, bacterial numbers increased only directly after inoculation. Thereafter, bacterial numbers decreased until an equilibrium was reached. This decrease was exponential on a log scale and could be described by the function Y = A + B − R ', where Y is the log number of rhizobial cells at time: T ; A represents the lgo of the final population size; B is the difference between the log (initial number of bacteria) and A ; R is the daily reduction factor of Y−A and t is time in days after inoculation. The final population sizes increased with increasing inoculum densities (10⁴−10⁸ bacteria/g soil). In sterilized soil, however, the populations increased up to an equilibrium, which was not affected by the inoculum density.
The final population sizes were higher in silt loam than in loamy sand in natural, as well as in sterilized soil. The final population size was reached earlier in natural silt loam than in loamy sand. Also the growth rate in sterilized soil was higher in silt loam than in loamy sand. The growth rate of low inoculum densities in silt loam was exponential and approximately the same as in yeast extract mannitol broth. The growth rate in loamy sand could be improved by incresing the bulk density of the soil from 1.0 to 1.4 g/cm³.