Do metal contamination and plant species affect microbial abundance and bacterial diversity in the rhizosphere of metallophytes growing in mining areas in a semiarid climate?

Journal of Soils and Sediments - Mining areas are low-quality habitats for macro- and microorganisms’ development, mainly due to the degradation of the soil quality by metal pollution. The...     

Ammonia-oxidizing archaea are more important than ammonia-oxidizing bacteria in nitrification and NO3 −-N loss in acidic soil of sloped land

As part of a long-term sloped land use experiment established in 1995 at Taoyuan Agro-ecosystem Research Station (111°26′ E, 28°55′ N) in China, soil samples were collected from three land use types, including cropland (CL), natural forest, and tea plantation. Quantitative polymerase chain reaction and terminal restriction fragment length polymorphism were used to determine the abundance and community composition of amoA-containing bacteria (AOB) and archaea (AOA). The results indicate that land use type induced significant changes in soil potential nitrification rate and community composition, diversity, and abundance of AOB and AOA. Both AOB and AOA community compositions were generally similar between upper and lower slope positions (UP and LP), except within CL. The LP soils had significantly (p?<?0.05) higher diversity and abundance of both AOB and AOA than in the UP. Potential nitrification rate was significantly correlated (p?<?0.05) with diversity and abundance of AOA, but not with AOB. Among land use types, the NO₃ ^? and amoA-containing AOA runoff loss was greatest in CL. Nitrate-N runoff loss was significantly correlated (p?<?0.05) with the loss of AOA amoA copies in the runoff water. Furthermore, relationships between NO₃ ^?-N runoff loss and abundance of AOA but not of AOB at both slope positions were significantly correlated (p?<?0.05). These findings suggest that AOA are more important than AOB in nitrification and NO₃ ^?-N runoff loss in acidic soils across sloped land use types.     

Do leaf traits and nitrogen supply affect decomposability rates of three Mediterranean species growing under different competition levels?

The effects of nitrogen addition on rates of litter decomposition of plants growing under different competition levels were assessed in a multifactorial glasshouse experiment. We established a two nitrogen-level treatment (control and fertilization) and three competition-level (plants growing alone, intra- and interspecific competition) experiment for Pinus pinea L., Pistacia lentiscus L. and Cistus salvifolius L. during one year. We collected leaves from different combinations at 3, 6 and 12 months and we established a 2-month microcosm experiment. We measured K_pot and different leaf and litter traits in order to test the hypothetical relationships between these traits and litter decomposability among the target species. Leaf nitrogen concentration was higher in plants growing under N-supply treatments but this supply only affected decomposition rates in the cases of P. pinea and P. lentiscus when grown alone. For P. pinea and C. salvifolius decay rate was higher in the fertilized treatment when growing alone. Leaf dry matter content was the leaf trait best related to litter decomposability. The results derived from the microcosm experiment provided evidence of the effect of some leaf and litter traits on litter decomposability and how some traits can give information about some important processes in ecosystems, such as decomposition.     

Soil characteristics and plant exotic species invasions in the Grand Staircase—Escalante National Monument,Utah, USA

The Grand Staircase—Escalante National Monument (GSENM) contains a rich diversity of native plant communities. However, many exotic plant species have become established, potentially threatening native plant diversity. We sought to quantify patterns of native and exotic plant species and cryptobiotic crusts (mats of lichens, algae, and mosses on the soil surface), and to examine soil characteristics that may indicate or predict exotic species establishment and success. We established 97 modified-Whittaker vegetation plots in 11 vegetation types over a 29,000 ha area in the Monument. Canonical correspondence analysis (CCA) and multiple linear regressions were used to quantify relationships between soil characteristics and associated native and exotic plant species richness and cover. CCA showed that exotic species richness was significantly (P<0.05) associated with soil P (r=0.84), percentage bare ground (r=0.71), and elevation (r=0.67). Soil characteristics alone were able to predict 41 and 46% of the variation in exotic species richness and cover, respectively. In general, exotic species invasions tend to occur in fertile soils relatively high in C, N and P. These areas are represented by rare mesic high-elevation habitats that are rich in native plant diversity. This suggests that management should focus on the protection of the rare but important vegetation types with fertile soils.     

Wood-decaying fungi in boreal forest: are species richness and abundances influenced by small-scale spatiotemporal distribution of dead wood?

We tested whether the spatiotemporal distribution of Norway spruce (Picea abies) logs influenced species richness and abundances of wood-decaying fungi in two 2-km² boreal forest study sites in southeastern Norway. According to the random sample null-hypothesis equally large subsamples of logs should be equally efficient in sampling fungi from a regional species pool. Based on 0.25-ha plots at 1-ha grid resolution, we compared plots with high and low densities of ‘new logs’ (decay stages 1-5) and plots with ‘old logs’ (decay stages 5-8) present or absent. Based on visible sporocarps, 45 fungus species, including 15 redlisted, were identified among 4151 logs. When rarefying species accumulation curves to the same number of logs, we found no difference in species richness between old forest plots having high and low densities of new logs, or between plots where old logs were present or absent. Curves from young forest revealed fewer species than in old forest. Multiple regression analysis of six redlisted and six common species corroborated the rarefaction analysis in showing that the probability of occurrence was independent of the spatiotemporal distribution of logs for all but two common species. Aside from the fact that more dead wood harboured more wood-decaying fungi, we conclude that the spatiotemporal distribution of dead wood was of minor importance in determining species richness and abundances at the scales of <1 ha and <100 years. This suggests that wood-decaying fungi are not dispersal-limited at these scales, and it offers an optional element in forest management.     

How does the application of different nitrification inhibitors affect nitrous oxide emissions and nitrate leaching from cow urine in grazed pastures?

Nitrous oxide (N₂O) is a potent greenhouse gas, and nitrate () is a water contaminant. In grazed grassland, the major source of both leaching and N₂O emissions is nitrogen (N) deposited in animal excreta, particularly in the urine. The objective of this study was to determine the effectiveness of two nitrification inhibitors: (i) a solution of dicyandiamide (DCD) and (ii) a liquid formulation of 3,4‐dimethylpyrazole phosphate (DMPP) for reducing N₂O emissions and leaching from urine patch areas in two grazed pasture soils under different environmental conditions. In the Canterbury Templeton soil, the nitrification rate of ammonium from the animal urine applied at 1000 kg N/ha was significantly decreased by the application of DCD (10 kg/ha) and DMPP (5 kg/ha). N₂O emissions, measured over a 3‐month period, from dairy cow urine applied to the Canterbury Templeton soil were 1.14 kg N₂O‐N/ha, and this was reduced to 0.43 and 0.39 kg N₂O‐N/ha by DCD and the liquid DMPP, respectively. These are equivalent to 62–66% reductions in the total N₂O emissions. Nitrate leaching losses from dairy cow urine applied to the Waikato Horotiu soil lysimeters were reduced from 628.6 kg ‐N/ha to 400.6 and 451.5 kg ‐N/ha by the application of DCD (10 kg/ha) or DMPP (1 kg/ha), respectively. There was no significant difference between the DCD solution and the liquid DMPP in terms of their effectiveness in reducing N₂O emissions or leaching under the experimental conditions of this study. These results suggest that both the liquid formulations of DCD and DMPP have the potential to be used as nitrification inhibitors to reduce N₂O emissions and leaching in grazed pasture soils.     

Do plant species with different growth strategies vary in their ability to compete with soil microbes for chemical forms of nitrogen?

We used dual labelled stable isotope (¹³C and ¹⁵N) techniques to examine how grassland plant species with different growth strategies vary in their ability to compete with soil microbes for different chemical forms of nitrogen (N), both inorganic and organic. We also tested whether some plant species might avoid competition by preferentially using different chemical forms of N than microbes. This was tested in a pot experiment where monocultures of five co-existing grassland species, namely the grasses Agrostis capillaris, Anthoxanthum odoratum, Nardus stricta, Deschampsia flexuosa and the herb Rumex acetosella, were grown in field soil from an acid semi-natural temperate grassland. Our data show that grassland plant species with different growth strategies are able to compete effectively with soil microbes for most N forms presented to them, including inorganic N and amino acids of varying complexity. Contrary to what has been found in strongly N limited ecosystems, we did not detect any differential uptake of N on the basis of chemical form, other than that shoot tissue of fast-growing plant species was more enriched in ¹⁵N from ammonium-nitrate and glycine, than from more complex amino acids. Shoot tissue of slow-growing species was equally enriched in ¹⁵N from all these N forms. However, all species tested, least preferred the most complex amino acid phenylalanine, which was preferentially used by soil microbes. We also found that while fast-growing plants took up more of the added N forms than slow-growing species, this variation was not related to differences in the ability of plants to compete with microbes for N forms, as hypothesised. On the contrary, we detected no difference in microbial biomass or microbial uptake of ¹⁵N between fast and slow-growing plant species, suggesting that plant traits that regulate nutrient capture, as opposed to plant species-specific interactions with soil microbes, are the main factor controlling variation in uptake of N by grassland plant species. Overall, our data provide insights into the interactions between plants and soil microbes that influence plant nitrogen use in grassland ecosystems.     

Methane oxidation,nitrification, and counts of methanotrophic bacteria in soils from a long-term fertilization experiment (”︁Ewiger Roggenbau” at Halle)

Aerobic soils are important sinks for atmospheric methane. CH₄ oxidation, mediated mainly by methanotrophic bacteria, is the responsible process, which is strongly inhibited by ammonium accessible for nitrification. An inhibitory effect immediately after fertilization as well as a long-term effect exists, which results from repeated ammonium applications and which is independent from the actual concentration of NH₄⁺-N in soil. This long-term effect could be caused by a shift in the microbial population of the soil. Thus, with soil samples from long-term fertilization treatments of the field experiment ”︁Ewiger Roggenbau” at Halle (Germany) incubation studies were conducted to investigate the interference between CH₄ oxidation and nitrification and to determine the cell numbers of methanotrophic bacteria. Including the treatments PK, NPK, and farmyard manure, which were established in 1878, a close negative correlation between CH₄ oxidation and net nitrification was found (r = —0.92). The CH₄ oxidation rates, determined with an initial concentration of 10 μl CH₄ l^—1, varied between 6.7 and 1.1 μg C kg^—1 d^—1 in the PK and NPK treatment, respectively. After application of NH₄Cl a strong inhibition of CH₄ oxidation occurred, which was 91%, 88%, 81%, and 63% in the treatments PK, NPK, FYM, and U (unfertilized), respectively. After a lag-phase of 2 to 3 weeks an incubation with high CH₄ concentrations (20 Vol.% CH₄) could induce CH₄ oxidizing activity in the NPK treatments under continuous rye or maize cropping. An increase of up to 40 times in comparison to the control under atmospheric CH₄ (2 μl CH₄ l^—1) was observed. A negative correlation (r = —0.74) existed between the CH₄ oxidation rates of the soils without recently applied NH₄⁺ and the numbers of methanotrophic bacteria, determined with the ”︁most probable number” method (MPN). Thus, the MPN technique is not suitable to characterize the physiologically active population of methanotrophic bacteria in soils, which oxidize CH₄ in the atmospheric concentration range. The results of this study suggest that in aerobic arable soils methanotrophic bacteria and not nitrifiers are responsible for CH₄ oxidation.     

Do farmers in Germany exploit the potential yield and nitrogen benefits from preceding oilseed rape in winter wheat cultivation?

Field experiments show that wheat grown after oilseed rape (OSR) achieves higher yield levels, while the nitrogen (N) application is reduced. However, field experiment data are based on few locations with optimised management. We analysed a large dataset based on farm data to assess the true extent of break crop benefits (BCB) for yield and N fertilisation within German commercial farming.

Across all German states and years, average yield of wheat preceded by OSR was 0.56 Mg ha^?1 higher than yield of wheat preceded by cereals (7.09 Mg ha^?1), although considerable variation between regions was observed. Mean N application across all states to wheat after OSR was 5 kg ha^?1 lower than to wheat after cereals. Choice of wheat types for different end uses (bread flour or animal feed) showed higher (0.77 Mg ha^?1) or lower (0.44 Mg ha^?1) BCB for yield of wheat cultivated after OSR compared with after cereals. The calculated BCB for yield and N fertilisation were lower than expected from dedicated field experiments and fertiliser recommendations. Thus the advantages of OSR as a preceding crop are generally utilised by commercial farmers in Germany but there is room for improvement.     

Do boundaries of soil animal and plant communities coincide? A case study of a Mediterranean forest in Russia

We studied the relationship between plant and soil animal communities by geostatistical analysis in a piedmont forest close to Novorossiysk (Southern Russia). Vegetation on the slope of a hill was an oak-ash-hornbeam forest, while the vegetation on the foot of the hill was a maple-ash-hornbeam forest. Two plots were studied each including both slope and foot habitats. On every plot samples collected formed a grid of 10 × 5 units with a 5 m distance between them. Soil macroinvertebrates were hand-sorted from the samples, and several soil parameters (soil, pebble, and litter mass, soil moisture) were measured.The analysis did not reveal coincidence between the boundaries of plant and soil animal communities on the bend of the hill. Soil animal communities of the plots were dominated by woodlice, diplopods, and insect larvae, reaching an abundance of 680–990 individuals m⁻² throughout the plots. Number of taxonomic groups per sample and overall animal abundance in the bend were the highest in both plots, whilst these parameters on the slope were the lowest. Variograms and maps of spatial distribution indicated that the boundary between soil animal communities was situated further up on the slope than the vegetation boundary. The size of the animal community was smaller than the size of plots sampled, what probably explained the lack of coincidence between the boundaries. There was a significant correlation between distribution of litter mass and parameters of soil animal communities, which was modulated by depth of soil layer and soil moisture. Soil parameters were more important for explaining boundaries between soil animal communities than plant communities in the forest considered.     

Do water regimes affect iron‐plaque formation and microbial communities in the rhizosphere of paddy rice?

Pot experiments were conducted to investigate the effect of soil water regimes on the formation of iron (Fe) plaque on the root surface of rice seedlings (Oryza sativa L.) and on the microbial functional diversity in a paddy soil. The rice seedlings were subjected to three moisture regimes (submergence, 100%, and 60% water‐holding capacity [WHC]), and were grown for 5 and 11 weeks. Aerobic lithotrophic Fe(II)‐oxidizing (FeOB) and acetate‐utilizing Fe(III)‐reducing bacteria (FeRB) in the rhizosphere and non‐rhizosphere soil were determined at 5 weeks using the most probable number (MPN) method. The carbon substrate use patterns of the microbial communities in the rhizosphere and non‐rhizosphere soil samples were determined at 11 weeks using Biolog‐GN2 plates. The amount of Fe plaque (per unit dry root weight) was much higher under submerged conditions than at lower soil moisture contents and decreased with plant age. There was a positive correlation between the amount of Fe plaque and phosphorus accumulated in the Fe plaque at both sampling times (r = 0.98 and 0.92, respectively, n = 12). Numbers of FeOB and FeRB in the submerged soil were lower than in aerobic soil, but by two orders of magnitude higher in the rhizosphere than in the bulk soil. On the other hand, the functional diversity of the rhizosphere microbial communities was much higher than that of the non‐rhizosphere soil, irrespective of soil water regimes. We conclude that soil flooding results in a decreased number and diversity of Fe‐oxidizing/reducing bacteria, while increasing the Fe‐plaque formation.     

The Rhagidiidae (Acari: Prostigmata) in NW Lapland: Could their assemblages be climate warming monitors related to environmental and habitat patterns?

Fifteen species of Palearctic and Holarctic Rhagidiidae inhabit the polar Fennoscandian mountain birch forest and tundra, but additional taxa are expected to be discovered. Their assemblages comprise 5–10 species. Of these, Rhagidia gigas, R. diversicolor and Poecilophysis pratensis are the most abundant and widely distributed in the forested subalpine (480–600 m a.s.l.) and transitional (500–650 m a.s.l.) altitudinal zones while Poecilophysis pseudoreflexa and Rhagidia longiseta are found in the low-(600–800 m a.s.l.) and mid-(800–960 m a.s.l.), and Rhagidia parvilobata in the high alpine (960–1025 m a.s.l.) zones. Ten species of the rhagidiid mites are common in the Fennoscandian tundra as well as the alpine tundra of the Ötztal Alps, North Tyrol. Patterns of richness and diversity in this group of mites are different in different altitudinal zones in NW Lapland and the Ötztal Alps. In contrast to the Alps, no endemic species were detected in Fennoscandia. The different altitudinal niches of most common mite species overlap, but some species of mites in the subalpine forest and the high alpine zone are altitudinal vegetation belt-specific and occupy different niches. Some species of mites are rare in all altitudinal vegetation belts.Rhagidia diversicolor, R. gigas, Poecilophysis pratensis and P. pseudoreflexa exhibited sufficient abundance, habitat and elevational specificity to be useful as indicator species of the subalpine to transitional as well as the low alpine to middle alpine altitudinal zones, respectively. Rhagidia parvilobata and Poecilophysis saxonica are indicators of the high alpine zone. Abundant species from the low subalpine forested zone as well as the high alpine zone are proposed as potential monitors for direct and indirect impact of climate warming. Summit mite invaders detecting current impact of climate warming were not discovered in the high alpine zone of the Fennoscandian oroboreal tundra.     

The Rhagidiidae (Acari: Prostigmata) in NW Lapland: Could their assemblages be climate warming monitors related to environmental and habitat patterns?

Fifteen species of Palearctic and Holarctic Rhagidiidae inhabit the polar Fennoscandian mountain birch forest and tundra, but additional taxa are expected to be discovered. Their assemblages comprise 5-10 species. Of these, Rhagidia gigas, R. diversicolor and Poecilophysis pratensis are the most abundant and widely distributed in the forested subalpine (480-600 m a.s.l.) and transitional (500-650 m a.s.l.) altitudinal zones while Poecilophysis pseudoreflexa and Rhagidia longiseta are found in the low-(600-800 m a.s.l.) and mid-(800-960 m a.s.l.), and Rhagidia parvilobata in the high alpine (960-1025 m a.s.l.) zones. Ten species of the rhagidiid mites are common in the Fennoscandian tundra as well as the alpine tundra of the Ötztal Alps, North Tyrol. Patterns of richness and diversity in this group of mites are different in different altitudinal zones in NW Lapland and the Ötztal Alps. In contrast to the Alps, no endemic species were detected in Fennoscandia. The different altitudinal niches of most common mite species overlap, but some species of mites in the subalpine forest and the high alpine zone are altitudinal vegetation belt-specific and occupy different niches. Some species of mites are rare in all altitudinal vegetation belts.Rhagidia diversicolor, R. gigas, Poecilophysis pratensis and P. pseudoreflexa exhibited sufficient abundance, habitat and elevational specificity to be useful as indicator species of the subalpine to transitional as well as the low alpine to middle alpine altitudinal zones, respectively. Rhagidia parvilobata and Poecilophysis saxonica are indicators of the high alpine zone. Abundant species from the low subalpine forested zone as well as the high alpine zone are proposed as potential monitors for direct and indirect impact of climate warming. Summit mite invaders detecting current impact of climate warming were not discovered in the high alpine zone of the Fennoscandian oroboreal tundra.     

Do elevated soil concentrations of metals affect the diversity and activity of soil invertebrates in the long‐term?

This study aimed to elucidate the response of diversity and activity of soil invertebrates to elevated soil metal concentrations that were a result of sewage sludge application. Field sampling of soil invertebrates was carried out from 2002 to 2004 at an experimental site established in 1982 to test the effects on crop production of metal contamination from sewage sludge applications with elevated concentrations of zinc (Zn), copper (Cu) and nickel (Ni) with certain treatments exceeding the current UK statutory limits for the safe use of sludge on land. At metal concentrations within the limits, none of the invertebrates sampled showed adverse effects on their abundance or overall community diversity (from Shannon–Weiner index). At concentrations above the limits, individual taxa showed sensitivity to different metals, but overall diversity was not affected. Earthworm abundance was significantly reduced at total Cu concentrations at and above 176 mg kg^?1, while nematode and enchytraeid abundances were sensitive to Cu and high Zn concentrations. Correspondingly, litter decomposition was lower in Zn and Cu treatments although there was no direct relationship between decomposition and soil invertebrate abundance or diversity. Such enduring changes in both soil biodiversity and biological activity around the current UK regulatory limits warrant further investigation to determine whether they indicate detrimental damage to soil functioning over the long‐term.     

Influence of rotation and tillage on forage maize productivity,weed species,and soil quality of a fine sandy loam in the cool–humid climate of Atlantic Canada

Reduced tillage systems may be an option to allow rapid crop establishment in areas constrained by a short growing season, but such methods need to be adapted to soil tillage requirement and crop establishment needs. Rotation and tillage studies were conducted during a 6-year period on a fine sandy loam (Podzol) with silage maize (Zea mays L.) under the cool, humid climate, and relatively short growing season of Prince Edward Island, Atlantic Canada. The objective was to compare a continuous maize rotation with a maize–barley (Hordeum vulgare L.) rotation, using both no-tillage and conventional mouldboard ploughing for the maize, and to evaluate treatment effects on maize growth and productivity, weed populations, and soil quality. Plant population and maize yield were not consistently influenced by the tillage or rotation treatments. Mean maize yield ranged from 7.2 to 7.7 Mg ha⁻¹. An increasing density of weeds over the 6-year period, especially perennial species, was evident under no-tillage, compared to mouldboard ploughing. Except for slight changes in soil pH, spatial variation in extractable soil P, and a higher level of organic C and labile forms of C (microbial biomass and mineralizable C), soil chemical quality was similar among treatments. An apparent decline in soil physical quality, as indicated by a reduction in macro-porosity volume and increase in soil penetration resistance below the 8 cm soil depth, was evident under the no-tillage at the end of the 6-year period. However, macro-pore continuity was less affected by a reduction in tillage, while field measurements of soil hydraulic conductivity increased under no-tillage compared to ploughing. The latter result may be related to the observed increase in earthworm population where tillage was reduced. Use of rotational tillage resulted in an intermediate soil physical condition between continuous no-tillage and ploughing. Overall, no-tillage appears a promising strategy to facilitate a fast and early establishment of maize on sandy loam soils in Atlantic Canada, but some ongoing monitoring of the soil physical condition would be required.     

Will future climate change threaten a range restricted endemic species, the quokka (Setonix brachyurus), in south west Australia?

Range-restricted species, such as regional endemics, possess traits that may make them particularly vulnerable to environmental change. The quokka, Setonix brachyurus, is a small macropod, endemic to south-western Australia and two adjacent islands. Climatic factors appear to play a role in defining the distribution of this species. Mainland populations are historically restricted to areas with an annual average rainfall in excess of 700 mm and their current distribution is almost completely confined within the 1000 mm rainfall isohyet. As such, the predicted increasing aridity of south-western Australia due to climate change is likely to threaten the continued persistence of the quokka on the mainland. To examine this possibility, we modelled the distribution of the quokka with Maxent using records of occurrence and a combination of historical climate (1961-1990) and habitat variables. Future projections of this distribution were then examined assuming two simple dispersal scenarios (zero and full migration) and three climate-change scenarios of increasing severity for 2030, 2050 and 2070. The predictive performance of the distribution model generated under historical climate conditions was high (AUC > 0.8), with annual precipitation contributing the most information to the model. Except for the low-severity climate-change scenario under the full dispersal assumption, the future projected distribution of quokka was shown to contract over time. The extent of range contraction tended to increase with the severity of the climate-change scenario, with the species predicted to lose almost all range by the year 2070 under the most extreme climate-change scenario. The results indicate the importance of identifying potential refuges for the quokka (i.e. areas where the species is predicted to persist) and defining management strategies to protect these areas from threatening processes.     

Does the influence of earthworms on water infiltration, nitrogen leaching and soil respiration depend on the initial soil bulk density? A mesocosm experiment with the endogeic species Metaphire posthuma

Soil compaction has a negative impact on both earthworm abundance and diversity. Recent studies, however, suggest that earthworm cast properties are not influenced by the initial soil bulk density. With time, earthworms could therefore transform soils with different bulk densities into a soil with the same physical state and thus with a similar ecological functioning. This study aimed to test this hypothesis in two laboratory incubation experiments. First, we measured the influence of soil bulk density (1.1 or 1.4?g?cm^?3) on the production of cast by the endogeic earthworm species Metaphire posthuma. In a second experiment, we investigated the effect of M. posthuma on water infiltration, NH ₄ ⁺ , and NO ₃ ^? leaching and soil respiration at the same two soil bulk densities. Although initially higher, earthworm casting activity in soil at 1.4?g?cm^?3 decreased until it reached the same level of activity as earthworms in soil at 1.1?g?cm^?3. This behavioral plasticity led to a transformation of compacted and loose soils, with their own functioning, to a third and similar state with similar hydraulic conductivity, nitrogen leaching, and soil respiration. The consequences for soil organization and soil functioning are discussed.