Relative role of deterministic and stochastic determinants of soil animal community: a spatially explicit analysis of oribatid mites

1. Ecologists are debating the relative role of deterministic and stochastic determinants of community structure. Although the high diversity and strong spatial structure of soil animal assemblages could provide ecologists with an ideal ecological scenario, surprisingly little information is available on these assemblages.
2. We studied species-rich soil oribatid mite assemblages from a Mediterranean beech forest and a grassland. We applied multivariate regression approaches and analysed spatial autocorrelation at multiple spatial scales using Moran's eigenvectors. Results were used to partition community variance in terms of the amount of variation uniquely accounted for by environmental correlates (e.g. organic matter) and geographical position. Estimated neutral diversity and immigration parameters were also applied to a soil animal group for the first time to simulate patterns of community dissimilarity expected under neutrality, thereby testing neutral predictions.
3. After accounting for spatial autocorrelation, the correlation between community structure and key environmental parameters disappeared: about 40% of community variation consisted of spatial patterns independent of measured environmental variables such as organic matter. Environmentally independent spatial patterns encompassed the entire range of scales accounted for by the sampling design (from tens of cm to 100 m). This spatial variation could be due to either unmeasured but spatially structured variables or stochastic drift mediated by dispersal. Observed levels of community dissimilarity were significantly different from those predicted by neutral models.
4. Oribatid mite assemblages are dominated by processes involving both deterministic and stochastic components and operating at multiple scales. Spatial patterns independent of the measured environmental variables are a prominent feature of the targeted assemblages, but patterns of community dissimilarity do not match neutral predictions. This suggests that either niche-mediated competition or environmental filtering or both are contributing to the core structure of the community. This study indicates new lines of investigation for understanding the mechanisms that determine the signature of the deterministic component of animal community assembly.

Photosynthetic pigments in soils from northern Victoria Land (continental Antarctica) as proxies for soil algal community structure and function

Although soil algae are among the main primary producers in most terrestrial ecosystems of continental Antarctica, there are very few quantitative studies on their relative proportion in the main algal groups and on how their distribution is affected by biotic and abiotic factors. Such knowledge is essential for understanding the functioning of Antarctic terrestrial ecosystems. We therefore analyzed biological soil crusts from northern Victoria Land to determine their pH, electrical conductivity (EC) water content (W), total and organic C (TC and TOC) and total N (TN) contents, and the presence and abundance of photosynthetic pigments. In particular, the latter were tested as proxies for biomass and coarse-resolution community structure. Soil samples were collected from five sites with known soil algal communities and the distribution of pigments was shown to reflect differences in the relative proportions of Chlorophyta, Cyanophyta and Bacillariophyta in these sites. Multivariate and univariate models strongly indicated that almost all soil variables (EC, W, TOC and TN) were important environmental correlates of pigment distribution. However, a significant amount of variation is independent of these soil variables and may be ascribed to local variability such as changes in microclimate at varying spatial and temporal scales. There are at least five possible sources of local variation: pigment preservation, temporal variations in water availability, temporal and spatial interactions among environmental and biological components, the local-scale patchiness of organism distribution, and biotic interactions. (C) 2009 Elsevier Ltd. All rights reserved.

CO2 uptake by a soil microcosm

Sequestration of CO2 via biological sinks is a matter of great scientific importance due to the potential lowering of atmospheric CO2. In this study, a custom built incubation chamber was used to cultivate a soil microbial community to instigate chemoautotrophy of a temperate soil. Real-time atmospheric CO2 concentrations were monitored and estimations of total CO2 uptake were made. After careful background flux corrections, 4.52 +/- 0.05 g CO2 kg I dry soil was sequestered from the chamber atmosphere over 40 h. Using isotopically labelled (CO2)-C-13 and GCMS-IRMS, labelled fatty acids were identified after only a short incubation, hence confirming CO2 sequestration for soil. The results of this in vivo study provide the ground work for future studies intending to mimic the in situ environment by providing a reliable method for investigating CO2 uptake by soil microorganisms.(C) 2012 Elsevier Ltd. All rights reserved.

Response of soil microbial communities to single and multiple doses of an organic pollutant

The effect of 100 μg 1,2-dichlorobenzene (1,2-DCB) g^-1 dry weight (dw) of soil introduced either as a single dose or multiple (10 fortnightly) doses of 10 μg g^-1 dw, on the microbial biomass, diversity of culturable bacterial community and the rate of 1,2-DCB mineralisation, were compared. After 22 weeks exposure both application regimes significantly reduced total bacterial counts and viable fungal hyphal length. The single dose had the greatest overall inhibitory effect, although the extent of inhibition varied throughout the study. Total culturable bacterial counts, determined after 22 weeks exposure showed little response to 1,2-DCB, but pseudomonad counts in single and multiple treatments were reduced to 9.7 and 0.147%, respectively, of the numbers detected in the control soil. The effect of 1,2-DCB application on the taxonomic composition of the culturable bacteria community was determined by fatty acid methyl ester (FAME) analysis. Compared to control soils, the single dose treatment had a lower percentage of Arthrobacter and Micrococcus. Multiple applications had a significant effect upon pseudomonad abundance, which represented only 2% of the identified community, compared to 45.6% in the control. The multi-dosed soils contained a high percentage of bacilli (> 25%). The effects of 1,2-DCB applications on the metabolic potential of the soil microbial community was determined by BIOLOG profiling. The number of carbon compounds utilised by the community in the multi-dosed soils (49 positives) was significantly less (P < 0.05) than detected in the single dose treatment (76) and control (66). The rate of 1,2-DCB mineralisation, determined by ¹⁴CO₂ production from radiolabelled [UL-¹⁴C] 1,2-DCB, declined throughout the study, and after 22 weeks was slightly but significantly (P < 0.05) lower in the multiply- than the singly-dosed soils. The differential response to 1,2-DCB treatments was attributed to its reduced bioavailability in soils after a single exposure, compared to multiple applications.

A review of rhizosphere carbon flow modelling

Rhizosphere processes play a key role in nutrient cycling in terrestrial ecosystems. Plant rhizodeposits supply low-molecular weight carbon substrates to the soil microbial community, resulting in elevated levels of activity surrounding the root. Mechanistic compartmental models that aim to model carbon flux through the rhizosphere have been reviewed and areas of future research necessary to better calibrate model parameters have been identified. Incorporating the effect of variation in bacterial biomass physiology on carbon flux presents a considerable challenge to experimentalists and modellers alike due to the difficulties associated with differentiating dead from dormant cells. A number of molecular techniques that may help to distinguish between metabolic states of bacterial cells are presented. The calibration of growth, death and maintenance parameters in rhizosphere models is also discussed. A simple model of rhizosphere carbon flow has been constructed and a sensitivity analysis was carried out on the model to highlight which parameters were most influential when simulating carbon flux. It was observed that the parameters that most heavily influenced long-term carbon compartmentalisation in the rhizosphere were exudation rate and biomass yield. It was concluded that future efforts to simulate carbon flow in the rhizosphere should aim to increase ecological realism in model structure.

Soil microbes and community coalescence

Community coalescence is a recently introduced term describing the interaction of entire communities and their environments. We here explicitly place the concept of community coalescence in a soil microbial context, exploring intrinsic and extrinsic drivers of such coalescence events. Examples of intrinsic events include the action of earthworms and the dynamics of soil aggregates, while extrinsic events are exemplified by tillage, flooding, litter-fall, outplanting, and the addition of materials containing microbial communities. Aspects of global change may alter the frequency or severity of coalescence events. We highlight functional consequences of community coalescence in soil, and suggest ways to experimentally tackle this phenomenon. Soil ecology as a whole stands to benefit from conceptualizing soil biodiversity in terms of dynamic coalescent microbial assemblages.

Microbial analysis of soil and groundwater from a gasworks site and comparison to a sequenced biological reactive barrier remediation process (SEREBAR)

Aims: To investigate the distribution of a polymicrobial community of biodegradative bacteria in (i) soil and groundwater at a former manufactured gas plant (FMGP) site and (ii) in a novel SEquential REactive BARrier (SEREBAR) bioremediation process designed to bioremediate the contaminated groundwater. Methods and Results: Culture-dependent and culture-independent analyses using denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction (PCR) for the detection of 16S ribosomal RNA gene and naphthalene dioxygenase (NDO) genes of free-living (planktonic groundwater) and attached (soil biofilm) samples from across the site and from the SEREBAR process was applied. Naphthalene arising from groundwater was effectively degraded early in the process and the microbiological analysis indicated a dominant role for Pseudomonas and Comamonas in its degradation. The microbial communities appeared highly complex and diverse across both the sites and in the SEREBAR process. An increased population of naphthalene degraders was associated with naphthalene removal. Conclusion: The distribution of micro-organisms in general and naphthalene degraders across the site was highly heterogeneous. Comparisons made between areas contaminated with polycyclic aromatic hydrocarbons (PAH) and those not contaminated, revealed differences in the microbial community profile. The likelihood of noncultured bacteria being dominant in mediating naphthalene removal was evident. Significance and Impact of the Study: This work further emphasizes the importance of both traditional and molecular-based tools in determining the microbial ecology of contaminated sites and highlights the role of noncultured bacteria in the process.

Soil resource supply influences faunal size-specific distributions in natural food webs

The large range of body-mass values of soil organisms provides a tool to assess the ecological organization of soil communities. The goal of this paper is to identify graphical and quantitative indicators of soil community composition and ecosystem functioning, and to illustrate their application to real soil food webs. The relationships between log-transformed mass and abundance of soil organisms in 20 Dutch meadows and heathlands were investigated. Using principles of allometry, maximal use can be made of ecological theory to build and explain food webs. The aggregate contribution of small invertebrates such as nematodes to the entire community is high under low soil phosphorus content and causes shifts in the mass-abundance relationships and in the trophic structures. We show for the first time that the average of the trophic link lengths is a reliable predictor for assessing soil fertility responses. Ordered trophic link pairs suggest a self-organizing structure of food webs according to resource availability and can predict environmental shifts in ecologically meaningful ways.

Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms

Rhizosphere microorganisms play an important role in soil carbon flow, through turnover of root exudates, but there is little information on which organisms are actively involved or on the influence of environmental conditions on active communities. In this study, a (CO2)-C-13 pulse labelling field experiment was performed in an upland grassland soil, followed by RNA-stable isotope probing (SIP) analysis, to determine the effect of liming on the structure of the rhizosphere microbial community metabolizing root exudates. The lower limit of detection for SIP was determined in soil samples inoculated with a range of concentrations of C-13-labelled Pseudomonas fluorescens and was found to lie between 10(5) and 10(6) cells per gram of soil. The technique was capable of detecting microbial communities actively assimilating root exudates derived from recent photo-assimilate in the field. Denaturing gradient gel electrophoresis (DGGE) profiles of bacteria, archaea and fungi derived from fractions obtained from caesium trifluoroacetate (CsTFA) density gradient ultracentrifugation indicated that active communities in limed soils were more complex than those in unlimed soils and were more active in utilization of recently exuded C-13 compounds. In limed soils, the majority of the community detected by standard RNA-DGGE analysis appeared to be utilizing root exudates. In unlimed soils, DGGE profiles from C-12 and C-13 RNA fractions differed, suggesting that a proportion of the active community was utilizing other sources of organic carbon. These differences may reflect differences in the amount of root exudation under the different conditions.

Primary assembly of soil communities: disentangling the effect of dispersal and local environment

It has long been recognised that dispersal abilities and environmental factors are important in shaping invertebrate communities, but their relative importance for primary soil community assembly has not yet been disentangled. By studying soil communities along chronosequences on four recently emerged nunataks (ice-free land in glacial areas) in Iceland, we replicated environmental conditions spatially at various geographical distances. This allowed us to determine the underlying factors of primary community assembly with the help of metacommunity theories that predict different levels of dispersal constraints and effects of the local environment. Comparing community assembly of the nunataks with that of non-isolated deglaciated areas indicated that isolation of a few kilometres did not affect the colonisation of the soil invertebrates. When accounting for effects of geographical distances, soil age and plant richness explained a significant part of the variance observed in the distribution of the oribatid mites and collembola communities, respectively. Furthermore, null model analyses revealed less co-occurrence than expected by chance and also convergence in the body size ratio of co-occurring oribatids, which is consistent with species sorting. Geographical distances influenced species composition, indicating that the community is also assembled by dispersal, e.g. mass effect. When all the results are linked together, they demonstrate that local environmental factors are important in structuring the soil community assembly, but are accompanied with effects of dispersal that may "override" the visible effect of the local environment.

Direct, positive feedbacks produce instability in models of interrelationships among soil structure, plants and arbuscular mycorrhizal fungi

Current conceptual models of reciprocal interactions linking soil structure, plants and arbuscular mycorrhizal fungi emphasise positive feedbacks among the components of the system. However, dynamical systems with high dimensionality and several positive feedbacks (i.e. mutualism) are prone to instability. Further, organisms such as arbuscular mycorrhizal fungi (AMF) are obligate biotrophs of plants and are considered major biological agents in soil aggregate stabilization. With these considerations in mind, we developed dynamical models of soil ecosystems that reflect the main features of current conceptual models and empirical data, especially positive feedbacks and linear interactions among plants, AMF and the component of soil structure dependent on aggregates. We found that systems become increasingly unstable the more positive effects with Type I functional response (i.e., the growth rate of a mutualist is modified by the density of its partner through linear proportionality) are added to the model, to the point that increasing the realism of models by adding linear effects produces the most unstable systems. The present theoretical analysis thus offers a framework for modelling and suggests new directions for experimental studies on the interrelationship between soil structure, plants and AMF. Non-linearity in functional responses, spatial and temporal heterogeneity, and indirect effects can be invoked on a theoretical basis and experimentally tested in laboratory and field experiments in order to account for and buffer the local instability of the simplest of current scenarios. This first model presented here may generate interest in more explicitly representing the role of biota in soil physical structure, a phenomenon that is typically viewed in a more process- and management-focused context. (C) 2011 Elsevier Ltd. All rights reserved.