Soil ecology is witnessing exponential growth in the number of studies using co-occurrence network analysis. Researchers reconstruct networks based on the co-occurrence of taxa or genes across soil ...samples at a wide range of geographic scales - from single aggregates to the whole planet - and taxonomic scopes, some studies targeting specific taxa or guilds to others surveying the whole microbiome as well as micro- and mesofauna. Co-occurrence networks can be very useful to extract simple patterns from complex datasets. Applications include the detection of abiotic and biotic factors that determine community structure, the identification of keystone taxa and their relationship to specific soil functions, and the inference of mechanisms of community assembly. However, networks are more and more often misused and serve as mere graphic tools with no attempt at hypothesis testing. In this perspectives article, we first review the main usage of co-occurrence network analysis in soil ecology during the last decade. We then discuss the applications and caveats of network analysis in soil ecology, leaving apart strictly methodological aspects of network reconstruction, which is beyond the focus of this article. Finally, we include recommendation guidelines – such as the possibility of informing networks with geographic, environmental and/or phylogenetic information – with the hope that this will facilitate network analysis to become a useful tool that helps elucidate meaningful patterns in soil ecology.
•Number of articles using co-occurrence network analysis has grown exponentially•Review usage and applications of networks in soil ecological communities•Detect main pitfalls and misuse of co-occurrence networks•Provide guidelines to extract meaningful ecological patterns from networks
Huge quantities of discarded fruits generated from greenhouse crops represent a worldwide environmental problem. The aim of this work was to assess the efficiency of vermicomposting as a recycling ...management option for biotransforming tomato-fruit wastes from greenhouses into an organic nutrient-rich product available for agricultural purposes. A pilot vermireactor was constructed. It was provided with a manure layer, where an initial population of
Eisenia fetida was introduced and fed continuously at a high organic loading rate (13.6
kg TOC m
−3
wk
−1) for 150
days. Vermicompost chemical and enzymatic parameters as well as the bacterial and fungal community structure were determined for 210
days (vermicomposting plus a maturation period). Earthworm biomass increased after 90
days, and then declined due to increasing pH, electrical conductivity and ammonium concentration. The temporal patterns of dehydrogenase, β-glucosidase, protease and urease were related to earthworm growth and the stabilization of organic matter. Bacterial DGGE profiles differed between the period of degradation of labile substrates and the maturation step. Fungal communities at the stage of maximum earthworm biomass differed most, suggesting a gut passage effect. The end product was chemically stable and enriched in nutrients, demonstrating that tomato-fruit wastes can be successfully vermicomposted into a valuable soil amendment. We suggest continuous-feeding vermicomposting as an environmentally sound management option for greenhouse wastes.
Phylogeny reflects genetic and phenotypic traits in Bacteria and Archaea. The phylogenetic conservatism of microbial traits has prompted the application of phylogeny-based algorithms to predict ...unknown trait values of extant taxa based on the traits of their evolutionary relatives to estimate, for instance, rRNA gene copy numbers, gene contents or tolerance to abiotic conditions. Unlike the 'macrobial' world, microbial ecologists face scenarios potentially compromising the accuracy of trait reconstruction methods, as, for example, extremely large phylogenies and limited information on the traits of interest. We review 990 bacterial and archaeal traits from the literature and support that phylogenetic trait conservatism is widespread through the tree of life, while revealing that it is generally weak for ecologically relevant phenotypic traits and high for genetically complex traits. We then perform a simulation exercise to assess the accuracy of phylogeny-based trait predictions in common scenarios faced by microbial ecologists. Our simulations show that ca. 60% of the variation in phylogeny-based trait predictions depends on the magnitude of the trait conservatism, the number of species in the tree, the proportion of species with unknown trait values and the mean distance in the tree to the nearest neighbour with a known trait value. Results are similar for both binary and continuous traits. We discuss these results under the light of the reviewed traits and provide recommendations for the use of phylogeny-based trait predictions for microbial ecologists.
Abstract
Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The ...potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.
This study describes the use of denaturing gradient gel electrophoresis (DGGE) and COMPOCHIP (i.e. a microarray targeting typical bacteria of stabilized organic materials and pathogenic bacteria) for ...investigating the bacterial communities of four different vermicomposts. These included a commercial vermicompost produced from cattle manure (CM) and three vermicomposts produced at pilot-scale by recycling: damaged tomato fruits (DT); olive-mill waste mixed with biosolids (OB); and winery wastes (WW). DGGE provided distinctive fingerprints of each vermicompost, which were statistically related to their particular chemical features. The comparison of the various vermicompost fingerprints showed that they contained bacterial communities with an average similarity coefficient of close to 80%. COMPOCHIP detected the presence of Sphingobacterium, Streptomyces, Alpha-Proteobacteria, Delta-Proteobacteria, and Firmicutes in all the vermicomposts. COMPOCHIP showed differences in the abundance of particular bacterial taxa among the vermicomposts, giving an idea about the usefulness of each vermicompost in the search for bacteria valuable to biotechnology. The joint use of DGGE and COMPOCHIP is a useful tool to compare vermicompost bacterial communities and to assess the potential of different vermicomposts as bioactive organic materials.
► Bacterial communities of four vermicomposts from different wastes were studied. ► Bacterial communities of the vermicomposts had an average similarity near 80%. ► Bacterial communities are mainly related with vermicomposts' chemical features. ► The presence of a core of common bacteria was evidenced in all vermicompost types. ► Vermicompost quality as bioactive material can be assessed by COMPOCHIP analysis.
The ecosystem functions performed by soil microbial communities can be indirectly altered by ecological disturbances that deeply modify abiotic factors. Fire, a widespread disturbance in nature, is ...well known to alter soil abiotic properties but we still ignore how these shifts are translated into changes in the structure of soil microbial communities and the ecosystem functions they deliver. The phylogenetic structure of soil bacterial communities has been shown to be a good predictor of ecosystem functioning, and therefore we used it as a measure linking the temporal variation of soil abiotic properties and ecosystem functions caused by an experimental fire in a Mediterranean shrubland. Fire immediately favoured a basal phylogenetic clade containing lineages that are able to thrive with high temperatures and to take advantage of the post-fire nutrient release. Later changes in the phylogenetic structure of the community were dominated by phyla from another basal clade that show competitive superiority coinciding with high levels of oxidizable carbon in soil. The phylogenetic structure of the bacterial community significantly explained not only microbial biomass, respiration and specific enzymatic activities related to C, N and P cycles but also the community-weighted mean number of 16S rRNA gene copies, an integrative proxy of several functions. While most of the ecosystem functions recovered one year after the fire, this was not the case of the structure of bacterial community, suggesting that functionally equivalent communities might be recovering the pre-disturbance levels of ecosystem performance.
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•Fire alters bacterial taxa distinctly depending on their position in the phylogeny.•Soil properties altered by fire determine the bacterial phylogenetic structure.•Bacterial communities vary with time since fire and impact ecosystem functions.•Ecosystem functions recover pre-fire levels faster than bacterial communities.
Under global change, how biological diversity and ecosystem services are maintained in time is a fundamental question. Ecologists have long argued about multiple mechanisms by which local ...biodiversity might control the temporal stability of ecosystem properties. Accumulating theories and empirical evidence suggest that, together with different population and community parameters, these mechanisms largely operate through differences in functional traits among organisms. We review potential trait-stability mechanisms together with underlying tests and associated metrics. We identify various trait-based components, each accounting for different stability mechanisms, that contribute to buffering, or propagating, the effect of environmental fluctuations on ecosystem functioning. This comprehensive picture, obtained by combining different puzzle pieces of trait-stability effects, will guide future empirical and modeling investigations.
The main mechanisms by which biodiversity affects the stability of ecosystem functions (dominant species, compensatory dynamics, and insurance effects) all act through the functional traits of organisms that form local communities.These mechanisms can be assessed using different components of trait value distributions within and between species collectively referred as trait probability density (TPD).Variation in local populations can result in overall changes in community structure, which may or may not be propagated into changes in ecosystem functions. The extent of such propagation depends on: (i) the extent of TPD shifts, and (ii) the overlap between response and effect traits, and these effects will vary depending on the biotic mechanisms being assessed.
1. Metal mining in drylands generates waste tailings with high toxicity, physical instability, as well as water and thermal stresses that hamper their biological colonization. This limits the ...restoration of ecosystem functions that are essential to re-integrate these artificial micro-deserts within the landscape matrix. 2. We assessed the functional role of local nurse plant species and their traits to restore ecosystem functions related to soil fertility, soil microbial productivity and the reduction of abiotic stress. We sampled 30 metalliferous tailings in a mining district from semi-arid Spain to detect nurse plant species and quantify their ability to promote essential functions from their establishment on the barren substrate up to the adult stage. 3. We found 11 plant species acting as nurses out of 102 species able to colonize barren soils. Ten nurses further triggered a cascade of effects increasing soil fertility and microbial productivity and/or lowering soil abiotic stress. 4. Plant species with larger life-forms and longer periods of establishment since tailing abandonment contributed the most to the promotion of ecosystem functions. C4 plant species developing root systems with lower intensivity and depth:laterality ratios, as well as leaves with lower carbon:nitrogen ratios (C:N) induced a faster recovery of ecosystem functions. 5. Synthesis and applications. We propose a protocol for selecting key species to be used in restoration programmes based on their ability to restore ecosystem functions under extremely stressful conditions. We encourage combination of multiple target species with complementary traits in order to reinforce the rehabilitation of ecosystem functions.
Microbes at Work Insam, Heribert; Franke-Whittle, Ingrid; Goberna, Marta
2010, 2009, 20091203, 2009-12-04
eBook, Book
Among the goals of environmentally sound waste treatment is the recycling of organic wastes. The most practiced options are composting and anaerobic digestion, both processes being carried out by ...microorganisms. This book provides an overview of the various ways microbes are doing their job and gives the reader an impression of their potential. The sixteen chapters of this book summarize the advantages and disadvantages of treatment processes, whether they are aerobic like composting or work without oxygen like anaerobic digestion for biogas (methane) production. These chapters show the potential of microorganisms to create valuable resources from otherwise wasted materials. These resources include profitable organic, humus-like soil conditioners or fertilizer components which are often suppressive to plant diseases. Composts may thus improve soil carbon sequestration, or support sustainable agriculture by reducing the need for mineral fertilizers or pesticides. If anaerobic digestion is used, the biogas produced may replace fossil fuels. Thus, proper biological waste treatment with the help of microorganisms should contribute to a reduction of anthropogenic greenhouse gas production.
Plant facilitation, an ecological interaction that benefits at least one species without harming the other, is increasingly used as a restoration tool. To restore degraded habitats under a ...facilitation framework, practitioners must correctly select both the benefactor (nurse) and the beneficiary (facilitated) species.
Based on community assembly and species coexistence theory, we propose selecting plant species that largely differ in a suite of functional traits so that competition is minimized and facilitation maximized due to functional complementarity. To apply this guideline in a pilot restoration experiment performed in metalliferous mine tailings in South‐Eastern Spain, we first built the plant–plant facilitative interaction network naturally occurring in a set of 12 tailings. After characterizing each species with 20 morphological and physiological traits, we verified that facilitative interactions were predominantly established between functionally distant species.
Then, we designed a sowing experiment combining 50 nurse‐facilitated species pairs separated by a wide range of functional distances. The success of seedling establishment significantly increased with the functional distance between the nurse and the facilitated plant species.
Synthesis and applications. We encourage the use of ecological facilitation together with trait‐based species selection to design restoration programmes based on the principle of increasing functional distance between target species. This method may not only promote the restoration of the plant cover but also impact paramount ecosystem functions, thus being an efficient low‐cost restoration practice in abiotically stressful ecosystems.
We encourage the use of ecological facilitation together with trait‐based species selection to design restoration programmes based on the principle of increasing functional distance between target species. This method may not only promote the restoration of the plant cover but also impact paramount ecosystem functions, thus being an efficient low‐cost restoration practice in abiotically stressful ecosystems.
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