Towards meaningful scales in ecosystem microbiome research

Peer reviewedPostprin

Rapid evolution of trait correlation networks during bacterial adaptation to the rhizosphere

There is a growing awareness that traits do not evolve individually but rather are organized as modular networks of covarying traits. Although the importance of multi-trait correlation has been linked to the ability to evolve in response to new environmental conditions, the evolvability of the network itself has to date rarely been assessed experimentally. By following the evolutionary dynamics of a model bacterium adapting to plant roots, we demonstrate that the whole structure of the trait correlation network is highly dynamic. We experimentally evolved Pseudomonas protegens, a common rhizosphere dweller, on the roots of Arabidopsis thaliana. We collected bacteria at regular intervals and determined a range of traits linked to growth, stress resistance, and biotic interactions. We observed a rapid disintegration of the original trait correlation network. Ancestral populations showed a modular network, with the traits linked to resource use and stress resistance forming two largely independent modules. This network rapidly was restructured during adaptation, with a loss of the stress resistance module and the appearance of new modules out of previously disconnected traits. These results show that evolutionary dynamics can involve a deep restructuring of phenotypic trait organization, pointing to the emergence of novel life history strategies not represented in the ancestral phenotype

Five Groups in the Genus Allovahlkampfia and the Description of the New Species Vahlkampfia bulbosis n.sp.

Heterolobosea is one of the major protist groups in soils. While an increasing number of soil heterolobosean species has been described, we have likely only scratched the surface of heterolobosean diversity in soils. Here, we expand this knowledge by morphologically and molecularly classifying four novel strains. One was identified as Naegleria clarki, while the remaining three strains had no identical Blast hit against GenBank and could only be reliably identified to the genus level: two strains as Allovahlkampfia spp. and one strain as Vahlkampfia sp. One Allovahlkampfia strain was most closely affiliated with Allovahlkampfia sp. Nl64 and the other strain was affiliated with ‘Solumitrus’ palustris, which is now named Allovahlkampfia palustris comb.nov. As there are only two valid species described within Allovahlkampfia, we combined all published sequences related to Allovahlkampfia and propose five new groups within this genus. The last strain was most closely related, but clearly distinct from, Vahlkampfia orchilla, based on DNA barcoding. As such, we propose this amoeba as a new species named Vahlkampfia bulbosis n.sp. Together, our study extends the described diversity of soil heteroloboseans through the description of a new Vahlkampfia species and by revising the morphologically and phylogenetically diverse genus Allovahlkampfia

Quantitative multiplex detection of plant pathogens using a novel ligation probe-based system coupled with universal, high-throughput real-time PCR on OpenArrays™

<p>Abstract</p> <p>Background</p> <p>Diagnostics and disease-management strategies require technologies to enable the simultaneous detection and quantification of a wide range of pathogenic microorganisms. Most multiplex, quantitative detection methods available suffer from compromises between the level of multiplexing, throughput and accuracy of quantification. Here, we demonstrate the efficacy of a novel, high-throughput, ligation-based assay for simultaneous quantitative detection of multiple plant pathogens. The ligation probes, designated Plant Research International-lock probes (PRI-lock probes), are long oligonucleotides with target complementary regions at their 5' and 3' ends. Upon perfect target hybridization, the PRI-lock probes are circularized via enzymatic ligation, subsequently serving as template for individual, standardized amplification via unique probe-specific primers. Adaptation to OpenArrays™, which can accommodate up to 3072 33 nl PCR amplifications, allowed high-throughput real-time quantification. The assay combines the multiplex capabilities and specificity of ligation reactions with high-throughput real-time PCR in the OpenArray™, resulting in a flexible, quantitative multiplex diagnostic system.</p> <p>Results</p> <p>The performance of the PRI-lock detection system was demonstrated using 13 probes targeting several significant plant pathogens at different taxonomic levels. All probes specifically detected their corresponding targets and provided perfect discrimination against non-target organisms with very similar ligation target sites. The nucleic acid targets could be reliably quantified over 5 orders of magnitude with a dynamic detection range of more than 10⁴. Pathogen quantification was equally robust in single target versus mixed target assays.</p> <p>Conclusion</p> <p>This novel assay enables very specific, high-throughput, quantitative detection of multiple pathogens over a wide range of target concentrations and should be easily adaptable for versatile diagnostic purposes.</p

Structural and functional variation in soil fungal communities associated with litter bags containing maize leaf

Soil fungi are key players in the degradation of recalcitrant organic matter in terrestrial ecosystems. To examine the organisms and genes responsible for complex organic matter degradation in soil, we tracked changes in fungal community composition and expressed genes in soil adjacent to mesh bags containing maize leaves undergoing decomposition. Using high-throughput sequencing approaches, changes in fungal community composition were determined by targeting 18S rRNA gene sequences, whereas community gene expression was examined via a metatranscriptomic approach. The majority of the 93 000 partial 18S rRNA gene sequences generated, were affiliated with the Ascomycota and Basidiomycota. Fungal diversity was at least 224 operational taxonomic units at the 97% similarity cutoff level. During litter degradation, the relative proportion of Basidiomycota increased, with a decrease in Ascomycota : Basidiomycota ratios over time. The most commonly detected decomposition-associated fungi included Agaricomycetes and Tremellales as well as unclassified Mucoromycotina. The majority of protein families found in the metatranscriptomic data were affiliated to fungal groups described to degrade plant-derived cellulose, such as Mucoraceae, Chaetomiaceae, Sordariaceae, Sebacinaceae, Tremellaceae, Psathyrellaceae and Schizophyllaceae. The combination of high-throughput rRNA gene-based and metatranscriptomic approaches provided perspectives into the organisms and genes involved in complex organic matter in soi

Protist feeding patterns and growth rate are related to their predatory impacts on soil bacterial communities

Predatory protists are major consumers of soil micro-organisms. By selectively feeding on their prey, they can shape soil microbiome composition and functions. While different protists are known to show diverging impacts, it remains impossible to predict a priori the effect of a given species. Various protist traits including phylogenetic distance, growth rate and volume have been previously linked to the predatory impact of protists. Closely related protists, however, also showed distinct prey choices which could mirror specificity in their dietary niche. We, therefore, aimed to estimate the dietary niche breadth and overlap of eight protist isolates on 20 bacterial species in plate assays. To assess the informative value of previously suggested and newly proposed (feeding-related) protist traits, we related them to the impacts of predation of each protist on a protist-free soil bacterial community in a soil microcosm via 16S rRNA gene amplicon sequencing. We could demonstrate that each protist showed a distinct feeding pattern in vitro. Further, the assayed protist feeding patterns and growth rates correlated well with the observed predatory impacts on the structure of soil bacterial communities. We thus conclude that in vitro screening has the potential to inform on the specific predatory impact of selected protists

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011

This report details the outcome of the 1st International Earth Microbiome Project Conference. The 2-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on the 14th-15th June 2011, and was hosted by BGI (formally the Beijing Genomics Institute). The conference was arranged as a formal launch for the Earth Microbiome Project, to highlight some of the exciting research projects, results of the preliminary pilot studies, and to provide a discussion forum for the types of technology and experimental approaches that will come to define the standard operating procedures of this project

Resource availability modulates biodiversity-invasion relationships by altering competitive interactions

Community diversity affects the survival of newly introduced species via resource competition. Competitive interactions can be modulated by resource availability and we hypothesized that this may alter biodiversity-invasion relationships. To study this, we assessed the growth of a bacterial invader, Ralstonia solanacearum, when introduced into communities comprised of one to five closely related resident species under different resource concentrations. The invader growth was then examined as a function of resident community richness, species composition and resource availability. We found that the relative density of the invader was reduced by increasing resident community richness and resource availability. Mechanistically, this could be explained by changes in the competitive interactions between the resident species and the invader along the resource availability gradient. At low resource availability, resident species with a high catabolic similarity with the invader efficiently reduced the invader relative density, while at high resource availability, fast-growing resident species became more important for the invader suppression. These results indicate that the relative importance of different resident community species can change dynamically along to resource availability gradient. Diverse communities could be thus more robust to invasions by providing a set of significant species that can take suppressive roles across different environments

Species traits interact with stress level to determine intraspecific facilitation and competition

Questions Flooding and drought stress are expected to increase significantly across the world and plant responses to these abiotic changes may be mediated by plant–plant interactions. Stress tolerance and recovery often require a biomass investment that may have consequences for these plant–plant interactions. Therefore, we questioned whether phenotypic plasticity in response to flooding and drought affected the balance between competition and facilitation for species with specific adaptations to drought or flooding. Location Utrecht University. Methods Stem elongation, root porosity, root:shoot ratio and biomass production were measured for six species during drought, well-drained and submerged conditions when grown alone or together with conspecifics. We quantified competition and facilitation as the ‘neighbour intensity effect’ directly after the 10-day treatment and again after a seven-day recovery period in well-drained conditions. Results Water stress, planting density and species identity interactively affected standardized stem elongation in a way that could lead to facilitation during submergence for species that preferably grow in wet soils. Root porosity was affected by the interaction between neighbour presence and time-step. Plant traits were only slightly affected during drought. The calculated neighbour interaction effect indicated facilitation for wetland species during submerged conditions and, after a period to recover from flooding, for species that prefer dry habitats. Conclusions Our results imply that changing plant–plant interactions in response to submergence and to a lesser extent to drought should be considered when predicting vegetation dynamics due to changing hydroclimatic regimes. Moreover, facilitation during a recovery period may enable species maladapted to flooding to persist