Do long-lived ants affect soil microbial communities?

This study was designed to test the hypothesis that desert ant species that build nests that remain viable at a particular point in space for more than a decade produce soil conditions that enhance microbial biomass and functional diversity. We studied the effects of a seed-harvester ant, Pogonomyrmex rugosus, and two generalist ant species, Aphaenogaster cockerelli and Myrmecocystus depilis, on soil microbial communities. Microbial biomass was higher in P. rugosus-modified soils than in reference soils when soil water content was higher than 3%. Microbial biomass was either higher in reference soils or exhibited no difference in reference soils and nest-modified soils of A. cockerelli and M. depilis. There were differences in microbial functional diversity and microbial community level physiological profiles (MicroResp method) between ant-nest-modified and reference soils of the three ant species on some sampling dates. Temporal patterns of soil microbial communities associated with the ant species resulted from differences in soil moisture, density, and species composition of the annual plant communities associated with the ant nests and in reference areas. Differences in annual plant communities associated with ant nests and surrounding areas resulted in different chemical inputs into the soil organic-matter pools. This study shows that generalizations about the effects of long-lived ant nests on soil biota in arid regions must consider feeding behaviors of the ant species and temporal patterns of rainfall.     

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...     

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.     

Short-term changes in chemical and microbial characteristics of paddy soil in response to consecutive addition of organic ameliorants in a rice–rice–vegetable rotation system

With regard of the problems of soil acidification and soil degradation caused by high intensive planting in south China, a 2-year pot experiment consisting of six harvests under a rice–rice–vegetable rotation cropping system was conducted to assess the effects of NPK+ rice straw (RS) and combined application of RS with peanut bran, biochar, and organic fertilizer on soil chemical and microbial characteristics in paddy soil. The control treatment received chemical fertilizer alone. Results showed that RS and the combination of RS with organic ameliorants, especially NPK+ rice straw + biochar (RSBC) treatment led to the greatest improvement of soil pH, soil organic carbon, microbial biomass carbon, and total nitrogen (TN) content, and urease (UE), acid phosphatase (ACP) and catalase (CAT) activities concurrently without yield sacrificing, which inferred that RSBC treatment could be an effective measure to alleviate soil acidification, boost carbon sequestration and nutrients content as well as soil enzyme activities in rice-rice-vegetable rotation system. Besides, Pearson’s correlation analysis showed that soil mineral nitrogen (N_min) content was negatively related to pH, and the available potassium (AK) content was positively related to UE and CAT activity but negatively related to ACP activity. Canonical correspondence analysis demonstrated the N_min and AK explained 27.2% and 13.7% of the variation in microbial species, respectively. Therefore, it is believed that soil N_min and AK content could be the primary factors of soil microbial properties under the rice-rice-vegetable rotation system.     

Soil microbial communities and enzyme activities in a reclaimed coastal soil chronosequence under rice–barley cropping

Purpose

A field experiment with a reclamation chronosequence under rice?Cbarley cropping was conducted to investigate soil enzyme activities and microbiology in a coastal saline soil. The aim of this study was to test whether changes in enzyme activity and microbial community structure are directly impacted by changes in soil pH, electrical conductivity (EC), and organic carbon (SOC) due to reclamation.

Materials and methods

The research area is located in south-eastern China. Four experimental sites were reclaimed in 1976, 1984, 1996, and 2006, respectively, and each site was divided into three plots, each of which was 22?m?×?10?m. Each year, the plots were planted with rice (cv Xiushui) in summer and barley (cv Yanmai) in winter. Soil pH and EC were determined in an aqueous suspension with a 1:5 ratio of soil and water. Soil organic carbon content was measured by dichromate oxidation with heating. Measured soil enzyme activities included catalase, urease, and protease. Soil microbial community structures were assessed using denaturing gradient gel electrophoresis.

Results and discussion

Reclamation under rice?Cbarley cropping reduced EC and pH, but increased SOC, the activities of catalase, urease and protease, and the cell numbers of bacteria, actinomycetes, and fungi, resulting in an increase in the bacterial community diversity. The enzyme activities and bacterial community diversity were significantly positively correlated with SOC, and negatively correlated with pH and EC. Five bacterial groups related to Gaetbulibacter, Sporosarcina, Flavobacterium, Aequorivita, and Gillisia, which have been associated with saline waters, did not appear in the soils that had been reclaimed prior to 1996.

Conclusions

Results of this field study suggest that soil properties which affect microbial activity such as EC, pH, and SOC significantly influence the activities of catalase, urease, and protease, and microbial community composition. More than 10?years after reclamation under rice?Cbarley cropping, EC had decreased and bacteria typically found in marine and saline environments had disappeared from the soil.     

Do bacterial and fungal communities in soils of the Bolivian Altiplano change under shorter fallow periods?

Traditional fallow periods in the Bolivian highlands are being shortened in an effort to increase short-term crop yields, with potential long-term impacts on soil microbial communities and their functions. In addition, native vegetation, such as Parasthrephia sp. or Baccharis sp. (both locally known as ‘thola’) are often removed as a fuel for cooking. We evaluated the effects of fallow period and thola on soils in 29 farmers' fields in two municipalities in the Bolivian Altiplano (Umala and Ancoraimes). Soil fungal and bacterial community responses were characterized using 454-pyrosequencing. Soils in Ancoraimes had significantly higher levels of organic matter, nitrogen and other macronutrients compared to Umala. Ancoraimes soils also supported more diverse fungal communities, whereas Umala had more diverse bacterial communities. Unexpectedly, the longer fallow periods were associated with significantly lower fungal diversity in Umala and lower bacterial diversity in Ancoraimes. Fungi assigned to genera Bionectria, Didymella, and Alternaria, and bacteria assigned to genera Paenibacillus, Segetibacter, and Modestobacter decreased in frequency with longer fallow period. The presence of thola was not associated with significantly different overall soil fungal or bacterial diversity, but was associated with higher frequency of some genera, such as Fusarium and Bradyrhizobium. Our results indicate that fallow period has a range of effects on soil communities, and that the removal of thola may impact the dynamics of these communities.     

Does oxidation affect the water functionality of myofibrillar proteins?

Water-binding properties of myofibrils extracted from porcine muscle, and added hemoglobin with and without exposure to H2O2, were characterized using low-field proton NMR T2 relaxometry. The effects of pH and ionic strength in the samples were investigated as pH was adjusted to 5.4, 6.2, and 7.0 and ionic strength was adjusted to 0.29, 0.46, and 0.71 M, respectively. The formation of dityrosine as a measure of oxidative protein cross-linking revealed a significant increase in dityrosine concentrations upon H2O2 activation. The formation of dityrosine was strongly pH-dependent and increased with decreasing pH. In addition, increased levels of thiobarbituric acid reactive substances were observed upon addition of H2O2, implying that lipid oxidation was enhanced, however, with a different oxidation pattern as compared to the myofibrillar proteins. Low-field NMR relaxation measurements revealed reduced T2 relaxation times upon H2O2 activation, which corresponds to reduced water-holding capacity upon oxidation. However, a direct relationship between degree of oxidation and T2 relaxation time was not observed with various pH values and ionic strengths, and further studies are needed for a complete understanding of the effect of oxidation on myofibrillar functionality.     

How different or similar are nematode communities between a paddy and an upland rice fields across a flooding-drainage cycle?

The paddy field is being recognised as a biodiversity hotspot fostering a variety of organisms. However, there are few studies on the ecology of paddy field nematodes. We characterised nematode communities in rice paddy fields by comparing them with upland fields of rice or soybean. We examined nematode communities of the top (0-15 mm) and second (15-50 mm) soil layers before flooding (March or April), during flooding (June or July) and during the draining period (October) 2007-2009. We found that the nematode community in the paddy was different than that in the upland fields during all periods. Rhabdolaimus, Tobrilus, Mesodorylaims and Monhysteridae characterised the top of the paddy and Hirschmanniella characterised the second layer of the paddy. Total nematode density was generally lower in the paddy than in the upland field. However, the density in the paddy top layer increased with time from the flooding period to the draining period, during which time it was about the same as (or even greater than) the peak density in the upland fields. The density in the second layer of the paddy remained lower than that in the top layer of the paddy throughout the time course. Community diversity values were generally greater in the paddy top layer than in the paddy second layer across the six sampling periods, but periodic differences between the paddy and upland fields or between soil layers were not significant. During the flooding period, the F/(F + B) (13-37) and Enrichment Index (17-38) values were lower in the paddy than in the upland fields (32-47, 37-74, respectively) to reflect that bacteria dominate over fungi with slow decomposition due to anaerobic conditions in the flooded paddy field. In addition, particularly in the top layer, the Maturity (2.0-2.4) and Structure Index (23-72) values were greater in the paddy than in the upland fields (1.7-2.1, 9-15, respectively), indicating a well-developed ecosystem under water. These unique nematode communities persisted during the draining period, but there was a rapid increase in opportunistic bacterivores, which increased the EI values. We suggest that bactivorous nematodes in the families Cephalobidae and Chronogasteridae, herbivores in the genus Hirschmanniella, and fungivores in the genus Filenchus may be specific to paddy field soil rather than to pond and lake sediments.     

Review Article. What are the nature and formation conditions of hydroxy‐interlayered minerals (HIMs) in soil?

Primary minerals of the parent material undergo weathering during the formation of terrestrial soils to varying extent. As a result, secondary minerals develop, which comprise, among many others, hydroxy‐interlayered minerals (HIMs). These minerals have formed by interlayering of hydroxy‐metal complexes (especially of Al³⁺, also Mg²⁺, Fe^2+/3+) into micas, expansible 2:1 phyllosilicates and forming oligomers, or by weathering of primary chlorite. The degree of interlayer filling and the stability of these fillings affect several physico‐chemical soil properties, for instance the cation exchange capacity. Although many studies have been conducted on formation, occurrence, and properties of HIMs in soil during the last decades, several challenges still exist. These challenges include analytical identification and quantification of HIMs in soil, the nature of the interlayer filling and the identification of favorable conditions in soil for the formation of HIMs. In order to deepen the understanding of formation, properties, and fate of HIMs in soil, we critically reviewed the available literature. Based on the review, we recommend using a new structural model that enables quantification of hydroxy‐interlayered smectite in soil by X‐ray diffractometry, laboratory experiments on the formation and preservation of different types of interlayers and considering the temporal and spatial dimension of the formation of HIMs in soil in more detail.     

Speciation and biochemical transformations of sulfur and copper in rice rhizosphere and bulk soil—XANES evidence of sulfur and copper associations

Purpose  

Contamination of heavy metals in soil and its subsequent accumulation along the food chain is a potential risk to human health. Cu speciation in soil–plant system, particularly on the availability to plant roots, has obtained great attention. X-ray absorption near-edge structure spectroscopy (XANES) provides information about the bonding of Cu soil components at the molecular scale. In paddy soils, changes of redox conditions led to microbially mediated sulfur transformation, thus affecting heavy metal behavior. The objective of this work was to investigate how sulfur transformation in a paddy soil affected Cu biogeochemical processes.     

A 3-year field investigation of impacts of Monsanto’s transgenic Bt-cotton NC 33B on rhizosphere microbial communities in northern China

Monsanto’s Bt-cotton NC 33B, planted in northern China for more than one decade, effectively controls cotton bollworms and decreases the use of chemical insecticides. Because of the concern about undesirable ecological side-effects of transgenic Bt-cottons, it is important to assess Bt-cotton NC 33B’s effects on soil microorganisms in this zone. Microbial communities in the rhizosphere soil of Bt and non-Bt cottons were monitored under field conditions by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints of eubacteria, fungi and actinomycetes at six growth stages after three-year cultivation. Results showed that the population sizes and community structures of eubacteria, fungi and actinomycetes in rhizosphere soil were markedly affected by natural variations in the environment related to cotton growth stages. However, there was no significant difference in eubacterial, fungal and actinomycete population size and community structures in rhizosphere soil between NC 33B and its non-transgenic parent. In general, Bt-cotton NC 33B did not show evident effects on microbial communities in the rhizosphere soil under field conditions after three-year cultivation. This study provides a theoretical basis for environmental impact monitoring of transgenic Bt cottons.     

Do sulfhydryl groups affect aggregation and gelation properties of ovalbumin?

The aim of this work is to evaluate the impact of sulfhydryl groups on ovalbumin aggregation and gelation. Ovalbumin was chemically modified to add sulfhydryl groups in various degrees. The rate of aggregation was not affected by the introduction of sulfhydryl groups, and disulfide bond formation was preceded by physical interactions. Hence, disulfide interactions may not be the driving force for the aggregation of ovalbumin. Investigation of the aggregates and gels by electron microscopy and rheology suggested that a critical number of sulfhydryl groups can be introduced beyond which the microstructure of the aggregates transforms from fibrillar into amorphous. Rheological studies further suggested that covalent networks, once formed, do not have the possibility to rearrange, reducing the possibility to attain a stronger network. These results show that, even though aggregation of ovalbumin may be primarily driven by physical interactions, formed disulfide bonds are important to determine the resulting aggregate morphology and rheological properties.     

Vertical distribution of microbial communities under the canopy of two legume bushes in the Tehuacán Desert,Mexico

Prosopis laevigata and Parkinsonia praecox are the most abundant perennial shrubs in the Tehuacán Desert, forming ’islands of fertility’ that dominate the alluvial terraces. Both species exhibit very similar phenology, with the timing of litter foliage being the only difference between them. P. praecox litter occurs shortly after the rains, while P. laevigata maintains its leaves until the next wet season. As degradable organic matter (OM) is one of the leading factors determining soil biota composition and activity, because of the OM provided by littering, we expected that the vertical distribution of the microbial community in the vicinity of the root zone of P. praecox would be higher in comparison to P. laevigata. One soil sampling was performed; during the rainy season in August, soil samples were collected from a 0–50-cm depth at 10-cm intervals, in the vicinity of the root canopy of four individual plants of each species and the interspaces between them. Soil moisture, organic matter, and counts of bacteria and fungi under shrubs were found to decrease from the upper to deeper layers. Respiratory activity was higher in the deeper layers (p < 0.01) in all three sampling sites. Total bacterial, fungal, and heterotrophic diazotrophs were found to be significantly (p < 0.001) more numerous under shrubs than in the interspace soil. No nitrogen-fixing bacteria were isolated from interplant soils in comparison to the soil samples collected beneath the shrubs. Heterotrophic diazotrophs significantly (p < 0.01) reduced more acetylene under P. praecox (29.0 nmol/g soil) than under P. laevigata (20.1 nmol/g soil). Although the microbial numbers were unaffected by differences in plant phenology, greater nitrogenase activity under P. praecox may influence nitrogen distribution in this arid environment. Due to the fact that only one sampling was undertaken, this study elucidates the differences in the microbial community between the two shrubs, but the dynamics in the above community could not be shown.     

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.     

For how long does the quality and quantity of residues in the soil affect the carbon compartments and CO<Subscript>2</Subscript>-C emissions?

Purpose

The mineralization/immobilization of nutrients from the crop residues is correlated with the quality of the plant material and carbon compartments in the recalcitrant and labile soil fractions. The objective of this study was to correlate the quality and quantity of crop residues incubated in the soil with carbon compartments and CO₂-C emission, using multivariate analysis.

Materials and methods

The experiment was conducted in factorial 4?+?2?+?5 with three replicates, referring to three types of residues (control, sugarcane, Brachiaria, and soybean), and two contributions of the crop residues in constant rate, CR (10 Mg ha^?1 residue), and agronomic rate, AR (20, 8, and 5 Mg ha^?1 residue, respectively, for sugarcane, soybean, and Brachiaria), evaluated five times (1, 3, 6, 12, and 48 days after incubation). At each time, we determined the CO₂-C emission, nitrogen and organic carbon in the soil, and the residues. In addition, the microbial biomass and water-soluble, labile, and humic substance carbons fractionated into fulvic acids, humic acids and humin were quantified.

Results and discussion

Higher CO₂-C emissions occurred in the soil with added residue ranging from 0.5 to 1.1 g CO₂-C m^?2 h^?1 in the first 6 days of incubation, and there was a positive correlation with the less labile organic soil fractions as well as residue type. In the final period, after 12 days of soil incubation, there was a higher relation of CO₂-C emission with carbon humin. The sugarcane and soybean residue (20 Mg ha^?1) promoted higher CO₂-C emission and the reduction of carbon residue. The addition of residue contributed to an 82.32 % increase in the emission of CO₂-C, being more significant in the residue with higher nitrogen availability.

Conclusions

This study shows that the quality and quantity of residue added to soil affects the carbon sequestration and CO₂-C emission. In the first 6 days of incubation, there was a higher CO₂-C emission ratio which correlates with the less stable soil carbon compartments as well as residue. In the final period of incubation, there is no effect of quality and quantity of residue added to soil on the CO₂-C emission.

     

Do organic inputs alter resistance and resilience of soil microbial community to drying?

Grassland ecosystems in south-eastern Australia are important for dairy and livestock farming. Their productivity relies heavily on water availability, as well as the ecosystem services provided by soil microbial communities including carbon and nutrient cycling. Management practices such as compost application are being encouraged as a means to improve both soil water holding capacity and fertility, thereby buffering against the impacts of increasing climate variability. Such buffering consists of two complementary processes: resistance, which measures the ability of an ecosystem to maintain community structure and function during a period of stress (such as drying); and resilience, which measures the ability of an ecosystem to recover community structure and function post-stress. We investigated the effects of compost on the resistance and resilience of the grassland soil ecosystem under drying and drying with rewetting events, in a terrestrial model ecosystem. Overall, compost addition led to an increase in soil moisture, greater plant available P and higher plant δ¹⁵N. Soil C:nutrient ratios, mineral N content (NH₄⁺ and NO₃⁻) and soil microbial PLFA composition were similar between amended and unamended soils. Rainfall treatment led to differences in soil moisture, plant above-ground and below-ground biomass, plant δ¹⁵N, soil mineral N content (NH₄⁺ and NO₃⁻) and microbial biomass C, N and P composition but had no effects on soil C:nutrient ratios, plant available P and soil microbial PLFA composition. There was little interaction between rainfall and compost. Generally, the soil microbial community was resistant and resilient to fluctuations in rainfall regardless of compost amendment. However, these properties of the soil microbial community were translated to resilience and not resistance in soil functions. Overall, the results below-ground showed much greater response to rainfall than compost amendment. Water was the key factor shaping the soil microbial community, and nutrients were not strong co-limiting factors. Future projections of increasing rainfall variability will have important below-ground functional consequences in the grassland, including altered nutrient cycling.     

Nitrogen pools and turnover in arable soils under different durations of organic farming: II: Source‐and‐sink function of the soil microbial biomass or competition with growing plants?

The following parameters were measured on seven field plots at 3 sites which had been under organic farming for different periods of time: mineral nitrogen (N _min) contents, in situ net nitrogen mineralization (N _net), soil microbial biomass carbon (C _mic), and nitrogen (N _mic) contents, and extractable organic N contents. The measurements were conducted every three weeks from spring 1995/1996 to autumn 1997. The objective was to test whether, under organic farming: 1) temporal fluctuations of N_mic contents over the course of the year are indicative for a source‐and‐sink function for plant‐available N of the soil microbial biomass, and 2) temporal variations in N_mic content can be related with in situ N_net or plant N uptake. N_min contents gradually increased after ploughing in autumn until late winter. During intensive plant growth in spring, values rapidly declined. In situ N_net fluctuated only moderately and reached high values during intensive plant growth (May—July) as well as after soil cultivation in autumn. The C_mic and N_mic contents generally were low in winter, increased in spring and reached maxima in late spring or summer. In spring, the increase in C_mic contents preceded the increase in N_mic contents, resulting in elevated C_mic:N_mic ratios until shooting of winter wheat. This corresponds to an uptake of available soil nitrogen by the plants at the expense of soil micro‐organisms. The subsequent increase in N_mic contents, coinciding with high plant N uptake rates, indicates an enhanced, plant‐induced N mobilization at that time. Possible mobilization mechanisms are discussed. Soil microbial biomass exerted a source‐and‐sink function for extractable organic N on some of the field plots. Estimates of in situ N_net measurements were neither correlated significantly with soil microbial biomass N, N_mic flux, N_mic turnover, nor with plant N uptake. Lower N_mic turnover rates on 41 years versus 3 years organically managed fields indicate a stabilizing effect of organic farming on soil microflora.     

Biodiversity and functioning of ecological communities — why is diversity important in some cases and unimportant in others?

The paper gives an overview of ecological theories and hypotheses that have been raised in order to predict diversity‐function relationships. In particular, those reasons are discussed that may explain the discrepancy between the theoretical expectation for widespread effects of diversity on functioning and the ambiguous empirical evidence for such effects. Structural differences in the ecology of plants, invertebrates, and micro‐organisms are considered which lead to differences in diversity‐function relationships among these groups of organisms. Four criteria are derived that determine diversity‐function relationships: (1) motility of the organisms under consideration, (2) decoupling of population persistence and functional activity in these organisms, (3) species richness of the organisms' community, and (4) equilibrium stability of the considered ecological process. From these criteria the authors predict that measurable effects of diversity on functioning are (a) likely to be found in plants and in micro‐organisms while they are (b) unlikely to be found in the soil fauna. They predict that diversity is (c) likely to affect primary production, soil energy turnover, and nutrient losses from the system, while it is (d) unlikely to durably influence litter decomposition rate. It is shown that these predictions are largely corroborated by empirical evidence compiled from the literature. The issue of spatial and temporal scale is briefly discussed.     

Can the increase of irrigation frequency improve the rate of water and salt migration in biochar-amended saline soil?

Journal of Soils and Sediments - It is difficult to leach salt into the deep layers of saline or sodic soils due to their poor permeability. The frequency of irrigation is a major factor affecting...