Resistance and resilience of zinc tolerant nitrifying communities is unaffected in long-term zinc contaminated soils

Zinc (Zn) tolerant nitrifying communities were previously identified in soil samples of a long-term Zn contaminated transect towards a galvanised pylon. We questioned whether Zn tolerance increased the vulnerability of the nitrifying communities to stressors. The influence of pesticide addition, freeze-thaw or dry-wet cycles on the soil nitrification (‘functional stability’) was assessed in a series of these soils representing a Zn contamination and Zn tolerance gradient. The immediate effect of the stressors to the nitrification (‘resistance’) and the residual effect after 3 weeks incubation (‘resilience’) were determined. Our results show that neither resistance nor resilience to these stressors was affected by adaptation of the nitrifying communities to elevated Zn concentrations in the long-term contaminated soils.     

The diet and food preferences of Onychiurus procampatus (Collembola) from upland grassland soils

Specimens of Onychiurus procampatus (Collembola) observed grazing on fungal mycelia were collected from the surface soil of three differently manged upland grasslands. A general trend of an increasing proportion of Collembola with a full gut was found along a gradient of reduced sheep management intensity, which was correlated with increased fungal biomass. In the laboratory, this collembolan showed a consistent order of preference for the mycelium of seven common fungal species isolated from the field sites.     

Decoupling plant-growth from land-use legacies in soil microbial communities

Differences in soil microbial communities between ex-arable and undisturbed soils are often assumed to reflect long-term legacies of agricultural practices. Ex-arable soils, however, are commonly dominated by different plant species than undisturbed soils making it difficult to separate the importance of land-use and plant-growth legacies. In a system where non-native plants dominate ex-arable soils, we decoupled land-use (ex-arable, undisturbed) and plant-growth (native, non-native) effects on soil microbial communities using a factorial sampling design. Soils were removed from 14 sites that formed a 52-year chronosequence of agricultural abandonment. Microbial abundance and composition were measured using whole-soil phospholipid fatty acid analyses and microbial activity was measured in a subset of samples using sole-carbon-source utilization analyses. We found that both non-native-cultivated and ex-arable soils were independently associated with lower microbial abundance and diversity than native and undisturbed soils. We also found a correlation between microbial abundance and age-since-agricultural abandonment in ex-arable/non-native-cultivated soils suggesting that non-native plant effects accumulate over time. Microbial activity was consistent with microbial abundance; microbial communities in non-native-cultivated, ex-arable soils were slow to respire most carbon sources. Our data suggests that agricultural practices create soil conditions that favor non-native plant growth and non-native plants maintain these conditions. Potential mechanisms explaining how non-natives create soils with small microbial communities and how small microbial communities may benefit non-natives are discussed.     

A comparison of the texture of grassland and eroded sandy soils from Shropshire, UK

In previous studies, periodic sampling of topsoils on runoff plots on sandy soils at the Hilton experimental site, Shropshire, UK, suggested erosion decreased the topsoil clay content and increased the coarse fraction. However, a comparison of soil and sediment properties suggested erosion selectively removed sand. Therefore, to cross-check the effects of erosion on soil properties, topsoil samples were collected from bare, eroded runoff plots and compared with samples from adjacent non-eroded grassland. Bare, eroded soil was stonier and particularly deficient in sand compared with grassed soil. Textural differences were very marked in the medium and coarse sands, especially the 0.5–1.0 mm fraction. On the basis of mean properties, the grassed soil was a very slightly stony loamy sand and the bare soil a slightly stony sandy loam. Soil organic matter was significantly less in the bare soils than the grassed soils and thus may have contributed to the higher erodibility of sands in bare soils.     

The impacts of individual plant species on rhizosphere microbial communities in soils of different fertility

To investigate the effects of individual plant species on microbial community properties in soils of differing fertility, a microcosm experiment was carried out using plant species representative of the dominant flora in semi-fertile temperate grasslands of northern England. Soil microbial biomass and activity were found to be significantly greater in the more fertile, agriculturally improved soil than in the less productive unimproved meadow soil. Differences in microbial community structure were also evident between the two soils, with fungal abundance being greater in the unimproved soil type. Individual plant species effects significantly differed between the two soils. Holcus lanatus and Anthoxanthum odoratum stimulated microbial biomass in the improved soil type, but negatively affected this measure in the unimproved soil. In both soil types, herb species generally had negative effects on microbial biomass. Patterns for microbial activity were less consistent, but as with microbial biomass, A. odoratum and H. lanatus promoted respiration, whereas the herbs negatively affected this measure. All plant species grown in the improved soil increased the abundance of fatty acids synthesised by bacteria (bacterial phospholipid fatty acid analysis) relative to bare soil, but they negatively impacted on this group of fatty acids in unimproved soil. Similarly, the abundance of the fungal fatty acid 18:26 was increased by all plants in the more fertile improved soil only, albeit non-significantly. Our data indicate that effects of plant species on microbial properties differ markedly in soils of differing fertility, making general predictions about how individual plants impact on soil properties difficult to make.     

Soil microbial biomass response to woody plant invasion of grassland

Woody plant proliferation in grasslands and savannas has been documented worldwide in recent history. To better understand the consequences of this vegetation change for the C-cycle, we measured soil microbial biomass carbon (C_mic) in remnant grasslands (time 0) and woody plant stands ranging in age from 10 to 130 years in a subtropical ecosystem undergoing succession from grassland to woodlands dominated by N-fixing trees. We also determined the ratio of SMB-C to soil organic carbon (C_mic/C_org) as an indicator of soil organic matter quality or availability, and the metabolic quotient (qCO₂) as a measure of microbial efficiency. Soil organic carbon (C_org) and soil total nitrogen (STN) increased up to 200% in the 0–15 cm depth increment following woody plant invasion of grassland, but changed little at 15–30 cm. C_mic at 0–15 cm increased linearly with time following woody plant encroachment and ranged from 400 mg C kg⁻¹ soil in remnant grasslands up to 600–1000 mg C kg⁻¹ soil in older (>60 years) woody plant stands. C_mic at 15–30 cm also increased linearly with time, ranging from 100 mg C kg⁻¹ soil in remnant grasslands to 400–700 mg C kg⁻¹ soil in older wooded areas. These changes in C_mic in wooded areas were correlated with concurrent changes in stores of C and N in soils, roots, and litter. The C_mic/C_org ratio at 0–15 cm decreased with increasing woody plant stand age from 6% in grasslands to <4% in older woodlands suggesting that woody litter may be less suitable as a microbial substrate compared with grassland litter. In addition, higher qCO₂ values in woodlands (0.8 mg CO₂-C g⁻¹ C_mic h⁻¹) relative to remnant grasslands (0.4 mg CO₂-C g⁻¹ C_mic h⁻¹) indicated that more respiration was required per unit of C_mic in wooded areas than in grasslands. Observed increases in C_org and STN following woody plant encroachment in this ecosystem may be a function of both greater inputs of poor quality C that is relatively resistant to decay, and the decreased ability of soil microbes to decompose this organic matter. We suggest that increases in the size and activity of C_mic following woody plant encroachment may result in: (a) alterations in competitive interactions and successional processes due to changes in nutrient dynamics, (b) enhanced formation and maintenance of soil physical structures that promote C_org sequestration, and/or (c) increased trace gas fluxes that have the potential to influence atmospheric chemistry and the climate system at regional to global scales.     

Soil microbial communities resistant to changes in plant functional group composition

The soil community is an often ignored part of research which links plant biodiversity and ecosystem functioning despite their influence on numerous functions such as decomposition and nutrient cycling. Few consistent patterns have been detected that link plant and soil community composition. We used a removal experiment in a northern Canadian grassland to examine the effects of plant functional group identity on soil microbial community structure and function. Plant functional groups (graminoids, legumes and forbs) were removed independently from plots for five growing seasons (2003-2007) and in the fifth year effects on the soil microbial community were examined using substrate-induced respiration (SIR - a measure of metabolic diversity) and phospholipid fatty acid analysis (PLFA - a measure of microbial community composition). Removal treatments were also crossed with both a fertilizer treatment and a fungicide treatment to determine if effects of functional group identity on the soil community were context dependent. Plant functional group identity had almost no effect on the soil microbial community as measured by either SIR or PLFA. Likewise, soil properties including total carbon, pH, moisture and nutrients showed a limited response to plant removals in the fifth year after removals. We found a direct effect of fertilizer on the soil community, with fertilized plots having decreased metabolic diversity, with a decreased ability to metabolize amino acids and a phenolic acid, but there was no direct soil microbial response to fungicide. We show that in this northern Canadian grassland the soil microbial community is relatively insensitive to changes in plant functional group composition, and suggest that in northern ecosystems, where plant material is only slowly incorporated into the soil, five growing seasons may be insufficient to detect the impact of a changing plant community on the soil microbes.     

Functional shifts of grassland soil communities in response to soil warming

In terrestrial ecosystems most carbon (C) occurs below-ground, making the activity of soil decomposer organisms critical to the global carbon cycle. Temperate grassland ecosystems, contain large, diverse and active soil meso- and macrofauna decomposer communities. Understanding the effects of climate change on their ecology offers a first step towards meaningful predictions of changes in soil organic carbon mineralisation.We examined the effects of soil warming on the abundance, diversity and ecology of temperate grassland soil fauna functional groups, ecosystem net CO₂ flux and respiration and plant above- and below-ground productivity in a 2-year plant-soil mesocosm experiment. Low voltage heating cable mounted on a framework of stainless steel mesh provided a constant 3.5 °C difference between control and warmed mesocosm soils.Results showed that this temperature increment had little effect on soil respiration and above-ground plant biomass. There was, however, a significant effect on the soil fauna due to warmer conditions and increased root growth, with significant decreases in the numbers in the large oligochaete groups and Prostigmata mites and the re-distribution of enchytraeids to deeper soil layers. Functional groups exhibited individualistic responses to soil warming, with the total disappearance of epigeic species in the case of the ecosystem engineers and an increased diversity of fungivorous mites that, together, produced significant changes in the composition and trophic structure of the fauna community.The observed switch towards a fungal driven food web has important implications for the fate of soil organic carbon in temperate ecosystems subjected to sustained warming. Accordingly, soil biology needs to be properly incorporated in C models to make better predictions of the fate of SOC under warmer scenarios.     

Development of pollution-induced community tolerance is linked to structural and functional resilience of a soil bacterial community following a five-year field exposure to copper

Copper (Cu) is accumulating in agricultural soils worldwide creating concern for adverse impacts on soil microbial communities and associated ecosystem services. In order to evaluate the structural and functional resilience of soil microbial communities to increasing Cu levels, we compared a Cu-adapted and a corresponding non-adapted soil microbial community for their abilities to resist experimental Cu pollution. Laboratory soil microcosms were set-up with either High-Cu soil from Cu-amended field plots (63 g Cu m⁻²) or with Low-Cu control soil from the same five-year field experiment. Laboratory treatments consisted of Cu amendments in the presence or absence of pig manure. Microbial activities (soil respiration, substrate-induced respiration, [³H]leucine incorporation), bacterial community structure (terminal restriction fragment length polymorphism, T-RFLP), community-level physiological profiles, and pollution-induced bacterial community tolerance (PICT detected using the [³H]leucine incorporation technique) were monitored for 12 weeks. The High-Cu and Low-Cu soil microbial communities initially exhibited almost identical structure and function and could only be distinguished from each other by their differential Cu tolerance. Experimental Cu pollution inhibited microbial activities, affected bacterial community structure, and induced further bacterial community tolerance to Cu. However, Low-Cu and High-Cu soil microbial communities showed essentially identical responses. Manure amendment did not protect against Cu toxicity and slightly increased Cu bioavailability as measured by a Cu-specific whole-cell bacterial biosensor. Our results indicate convergence of bacterial community structure and function in the High-Cu and Low-Cu soils during the five-year field experiment. We conclude that soil bacterial communities can exhibit structural and functional resilience to a five-year Cu exposure by virtue of their ability to develop Cu tolerance without affecting overall community structure. The observed increased Cu tolerance may involve phenotypic adaptation or selection at the micro-diversity level, for example an increased proportion of Cu-resistant strains within each bacterial species, which go undetected by T-RFLP community fingerprinting. Finally, our results indicate that Cu-dissolved organic matter complexes contribute to microbial toxicity in manure-amended soils implying that free Cu may comprise a poor predictor of metal toxicity.     

Combined effects of compost containing Sulfamethazine and zinc on pakchoi (Brassica chinensis L.) growth,soil sulfonamide resistance genes,and microbial communities

To understand the ecotoxicity of antibiotics and heavy metals in soil, 5% (w/w) composts containing different concentrations of sulfamethazine (SMZ) and/or zinc (Zn) were applied to soil to investigate their effects on pakchoi (Brassica chinensis L.) growth, soil sulfonamide resistance genes (SRGs: sul1, sul2, and dfrA7), and soil microbial communities. Composts containing less than 1.0 mg SMZ kg^–1 or less than 2.8 g Zn kg^–1 promoted pakchoi growth and the metabolic activity of soil microbial communities. Compared with the control, the absolute abundances (AAs) of soil SRGs significantly increased by 0.85–4.54 times with 50.6 μg kg^–1 SMZ treatment (P < 0.05), the AA of sul2 increased by 166% with 248.8 mg Zn kg^–1 treatment. The combination treatments with 19.8 μg SMZ kg^–1 and 179.9 mg Zn kg^–1 in soil had synergistic stimulatory effects on pakchoi growth, soil SRGs and microbial metabolism, whereas 53.5 μg SMZ kg^–1 and 262.1 mg Zn kg^–1 had an opposite effect. Pearson’s correlation analysis showed that carbon metabolism by soil microorganisms had significant positive correlations with shoot height of pakchoi (r = 0.84, P < 0.05) and AAs of SRGs (r > 0.80, P < 0.05).