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Microbial communities have a central role in ecosystem processes by driving the Earth’s biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution approach to analyze the functional consequences of diversity loss. A trait-centered approach was embraced using the denitrifiers as model guild due to their role in nitrogen cycling, a major ecosystem service. How various diversity metrics related to richness, eveness and phylogenetic diversity of the soil denitrifier community were affected by the removal experiment was assessed by 454 sequencing. As expected, the diversity metrics indicated a decrease in diversity in the 1/10 3 and 1/10 5 dilution treatments compared with the undiluted one. However, the extent of dilution and the corresponding reduction in diversity were not commensurate, as a dilution of five orders of magnitude resulted in a 75% decrease in estimated richness. This reduction in denitrifier diversity resulted in a significantly lower potential denitrification activity in soil of up to 4–5 folds. Addition of wheat residues significantly increased differences in potential denitrification between diversity levels, indicating that the resource level can influence the shape of the microbial diversity–functioning relationship. This study shows that microbial diversity loss can alter terrestrial ecosystem processes, which suggests that the importance of functional redundancy in soil microbial communities has been overstated.

Copper has been successfully used in the sulfate form as a fungicide to control grapevine diseases since 150 years, yet high Cu accumulation in vineyards may alter soil life. Although actual Cu additions are about tenfold lower than 50 years ago, the use of Cu in the context of the agroecological transition is still debated. Indeed, copper is one of the rare pesticides allowed for organic farming. Therefore, we performed a meta-analysis on Cu ecotoxicity by selecting 19 articles out of 300 articles relevant to copper and soil biological quality. Results show that microbial activity decreased by 30% when more than 400 kg of Cu was applied yearly per ha. Nematodes abundance remained unchanged for copper application up to 3200 kg/ha/year. Collembola and enchytraeid reproduction declined by 50% after application of 400 and 1895 kg Cu/ha/year, respectively. Earthworm biomass was reduced by 15% after application of 200 kgCu/ha/year. For soil Cu levels higher than 200 kg Cu/ha, microbial respiration decreased by 50% and no effect was observed on collembola. Overall, while toxicity is observed, the corresponding literature investigations involved Cu levels that are at least 50 times higher than the dose of 4 kg Cu/ha/year currently authorized by the European Commission for viticulture. As a consequence, applying copper at 4 kg/ha/year should not modify substantially soil biological quality and functions.

The productivist model implemented after the second world war has succeeded in improving production to meet growing demands for food, but it has also deeply affected soil physicochemical properties, as well as of aboveground and belowground biodiversity. Alternative farming systems such as organic farming, biodynamic farming and soil conservation farming are actually developing to enhance the sustainability of farming systems. Although the impact of agricultural practices on soil ecological quality is well known, there is little knowledge on the impact of the different farming systems as a whole. Here, we analysed the impact of the main farming systems on soil biodiversity and functioning, reported in about 100 scientific publications. We found that conventional, organic, and biodynamic systems are the most widely studied, whereas soil conservation farming is poorly documented. Soil biological indicators are improved by ca. 70% in organic farming and biodynamic farming relative to conventional farming. 43% of soil bioindicators are improved in biodynamic farming relatively to organic farming. Soil conservation farming scores better than conventional farming for 57% of the indicators. Therefore, biodynamic farming displays the highest soil ecological quality, followed by organic farming, soil conservation farming and, last, conventional farming. Organic fertilisation and longer crop rotations are the most favourable practices, whereas pesticides and soil tillage are the most deleterious ones. The review also evidences a lack of studies on soil conservation farming and on bioindicators of the soil fauna.

Evaluating the quality of ecosystems in terms of biological patrimony and functioning is of critical importance in the actual context of intensified human activities. Microbial diversity is commonly used as a bioindicator of ecosystems functioning. However, there is a lack of sensitivity of microbial diversity indicators in the case of moderate and chronic environmental degradation, such as atmospheric deposition of pollutants, agricultural practices, diffuse pollution by wastewater and climate change. As a consequence, there is a need for alternative bioindicators of soils and water quality. Here, we discuss the interest of adopting a more integrative approach based on biotic interaction networks beyond the simple diversity indicators. We review how the various biotic interactions can be integrated in the various microbial networks such as trophic, mutualistic and co-occurrence networks. Then we discuss the efficiency of microbial networks and associated metrics to detect changes in microbial communities. We conclude that the connectance, the number of links and the average degree of co-occurrence networks could vary from 10 to 50% in response to minor perturbations when microbial diversity parameters remain stable. Finally, we analyze studies that aimed at linking microbial networks and activity to evaluate the potential of such networks for providing simple and operational indicators of ecosystem quality and functioning.

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.

Soil microbial communities undergo rapid shifts following modifications in environmental conditions. Although microbial diversity changes may alter soil functioning, the in situ temporal dynamics of microbial diversity is poorly documented. Here, we investigated the response of fungal and bacterial diversity to wheat straw input in a 12-months field experiment and explored whether this response depended on the soil management history (grassland vs. cropland). Seasonal climatic fluctuations had no effect on the diversity of soil communities. Contrastingly fungi and bacteria responded strongly to wheat regardless of the soil history. After straw incorporation, diversity decreased due to the temporary dominance of a subset of copiotrophic populations. While fungi responded as quickly as bacteria, the resilience of fungal diversity lasted much longer, indicating that the relative involvement of each community might change as decomposition progressed. Soil history did not affect the response patterns, but determined the identity of some of the populations stimulated. Most strikingly, the bacteria Burkholderia, Lysobacter and fungi Rhizopus, Fusarium were selectively stimulated. Given the ecological importance of these microbial groups as decomposers and/or plant pathogens, such regulation of the composition of microbial successions by soil history may have important consequences in terms of soil carbon turnover and crop health.

Studying the ecology of photosynthetic microeukaryotes and prokaryotic cyanobacterial communities requires molecular tools to complement morphological observations. These tools rely on specific genetic markers and require the development of specialised databases to achieve taxonomic assignment. We set up a reference database, called µgreen-db, for the 23S rRNA gene. The sequences were retrieved from generalist (NCBI, SILVA) or Comparative RNA Web (CRW) databases, in addition to a more original approach involving recursive BLAST searches to obtain the best possible sequence recovery. At present, µgreen-db includes 2,326 23S rRNA sequences belonging to both eukaryotes and prokaryotes encompassing 442 unique genera and 736 species of photosynthetic microeukaryotes, cyanobacteria and non-vascular land plants based on the NCBI and AlgaeBase taxonomy. When PR 2 /SILVA taxonomy is used instead, µgreen-db contains 2,217 sequences (399 unique genera and 696 unique species). Using µgreen-db, we were able to assign 96% of the sequences of the V domain of the 23S rRNA gene obtained by metabarcoding after amplification from soil DNA at the genus level, highlighting good coverage of the database. µgreen-db is accessible at http://microgreen-23sdatabase.ea.inra.fr .

Background The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool. Results BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups. Conclusions The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.

Soil microbial communities respond quickly to natural and/or anthropic-induced changes in environmental conditions. Metagenomics allows studying taxa that are often overlooked in microbiota studies, such as protists or viruses. Here, we employed metagenomics to characterise microbial successions after wheat straw input in a 4-month in-situ field study. We compared microbial successions patterns with those obtained by high throughput amplicon sequencing on the same soil samples to validate metagenomics as a tool for the fine analysis of microbial population dynamics in situ. Taxonomic patterns were concordant between the two methodologies but metagenomics allowed studying all the microbial groups simultaneously. Notably, our results evidenced that each domain displayed a specific dynamic pattern after wheat straw amendment. For instance, viral sequences multiplied in the early phase of straw decomposition, in parallel to copiotrophic bacteria, suggesting a “kill-the-winner” pattern that, to our knowledge, had not been observed before in soil. Altogether, our results highlighted that both inter and intra-domain trophic interactions were impacted by wheat amendment and these patterns depended on the land use history. Our study highlights that top-down regulation by microbial predators or viruses might play a key role in soil microbiota dynamics and structure.

Summary Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15 000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.