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Journal ArticleDOI

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe.

TL;DR: It is suggested that positive effects of particular microbial taxa on multifunctionality resistance could potentially be controlled by altering soil pH, and insights are provided into the importance of microbial community composition for buffering effects of global change in drylands worldwide.
Abstract: The relationship between soil microbial communities and the resistance of multiple ecosystem functions linked to C, N and P cycling (multifunctionality resistance) to global change has never been assessed globally in natural ecosystems. We collected soils from 59 dryland ecosystems worldwide to investigate the importance of microbial communities as predictor of multifunctionality resistance to climate change and nitrogen fertilisation. Multifunctionality had a lower resistance to wetting-drying cycles than to warming or N deposition. Multifunctionality resistance was regulated by changes in microbial composition (relative abundance of phylotypes) but not by richness, total abundance of fungi and bacteria or the fungal: bacterial ratio. Our results suggest that positive effects of particular microbial taxa on multifunctionality resistance could potentially be controlled by altering soil pH. Together, our work demonstrates strong links between microbial community composition and multifunctionality resistance in dryland soils from six continents, and provides insights into the importance of microbial community composition for buffering effects of global change in drylands worldwide.
Citations
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Journal ArticleDOI
TL;DR: It is shown that global change Factors affect microbial diversity inconsistently; negative effects are most likely for global change factors that affect soil pH.
Abstract: Biodiversity on the Earth is changing at an unprecedented rate due to a variety of global change factors (GCFs). However, the effects of GCFs on microbial diversity is unclear despite that soil microorganisms play a critical role in biogeochemical cycling. Here, we synthesize 1235 GCF observations worldwide and show that microbial rare species are more sensitive to GCFs than common species, while GCFs do not always lead to a reduction in microbial diversity. GCFs-induced shifts in microbial alpha diversity can be predominately explained by the changed soil pH. In addition, GCF impacts on soil functionality are explained by microbial community structure and biomass rather than the alpha diversity. Altogether, our findings of GCF impacts on microbial diversity are fundamentally different from previous knowledge for well-studied plant and animal communities, and are crucial to policy-making for the conservation of microbial diversity hotspots under global changes.

271 citations

Journal ArticleDOI
TL;DR: Compared with inorganic fertilization, the application of organic fertilizer improved the soil multifunctionality, which positively correlated with the both bacterial and fungal diversity and indicated that rare microbial taxa had an over-proportional role in biological processes.
Abstract: Soil microbial communities play an essential role in driving multiple functions (i.e., multifunctionality) that are central to the global biogeochemical cycles. Long-term fertilization has been reported to reduce the soil microbial diversity, however, the impact of fertilization on multifunctionality and its relationship with soil microbial diversity remains poorly understood. We used amplicon sequencing and high-throughput quantitative-PCR array to characterize the microbial community compositions and 70 functional genes in a long-term experimental field station with multiple inorganic and organic fertilization treatments. Compared with inorganic fertilization, the application of organic fertilizer improved the soil multifunctionality, which positively correlated with the both bacterial and fungal diversity. Random Forest regression analysis indicated that rare microbial taxa (e.g. Cyanobacteria and Glomeromycota) rather than the dominant taxa (e.g. Proteobacteria and Ascomycota) were the major drivers of multifunctionality, suggesting that rare taxa had an over-proportional role in biological processes. Therefore, preserving the diversity of soil microbial communities especially the rare microbial taxa could be crucial to the sustainable provision of ecosystem functions in the future.

207 citations

Journal ArticleDOI
TL;DR: The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession.
Abstract: Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown. Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms. The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies.

172 citations

Journal ArticleDOI
TL;DR: Both bacterial/archaeal and fungal communities were shaped by the same Edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/ archaeal communities than onFungal communities, as demonstrated by (partial) Mantel tests.
Abstract: Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.

159 citations


Cites background or result from "Soil microbial communities drive th..."

  • ...…composition in regulating multiple soil processes, soil microbial diversity also plays a pivotal role in maintaining ecosystem multifunctionality (Delgado-Baquerizo et al., 2017b, 2016; Wagg et al., 2014), corroborating the strong correlations between bacterial/archaeal/fungal richness/diversity…...

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  • ...…soil functions, in recent years there is an emerging field of research began to investigate how microbial communities maintain ecosystem multifunctionality based on both observational and manipulative studies (Bastida et al., 2016; Delgado-Baquerizo et al., 2017a, 2017b; 2016; Wagg et al., 2014)....

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  • ...Interestingly, no effects of microbial richness or diversity on the soil C process matrix or on microbial respiration or CUE were detected, in accordance with previous field study that showed no relation between basal respiration with bacterial richness (Delgado-Baquerizo et al., 2017b)....

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  • ...We also observed substantial associations between microbial richness/ diversity and soil enzyme patterns and single soil enzyme activities (Tables S6A and B), in line with findings from previous soil multifunctionality studies (Delgado-Baquerizo et al., 2017b, 2017a)....

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Journal ArticleDOI
TL;DR: It is found that in more mesic sites with high SOC concentrations, soil priming effects are more likely to be negative, with important implications for the improvement of C cycling models under global change scenarios.
Abstract: Identifying the global drivers of soil priming is essential to understanding C cycling in terrestrial ecosystems. We conducted a survey of soils across 86 globally-distributed locations, spanning a wide range of climates, biotic communities, and soil conditions, and evaluated the apparent soil priming effect using 13C-glucose labeling. Here we show that the magnitude of the positive apparent priming effect (increase in CO2 release through accelerated microbial biomass turnover) was negatively associated with SOC content and microbial respiration rates. Our statistical modeling suggests that apparent priming effects tend to be negative in more mesic sites associated with higher SOC contents. In contrast, a single-input of labile C causes positive apparent priming effects in more arid locations with low SOC contents. Our results provide solid evidence that SOC content plays a critical role in regulating apparent priming effects, with important implications for the improvement of C cycling models under global change scenarios.

132 citations

References
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Journal ArticleDOI
01 Oct 2001
TL;DR: Internal estimates monitor error, strength, and correlation and these are used to show the response to increasing the number of features used in the forest, and are also applicable to regression.
Abstract: Random forests are a combination of tree predictors such that each tree depends on the values of a random vector sampled independently and with the same distribution for all trees in the forest. The generalization error for forests converges a.s. to a limit as the number of trees in the forest becomes large. The generalization error of a forest of tree classifiers depends on the strength of the individual trees in the forest and the correlation between them. Using a random selection of features to split each node yields error rates that compare favorably to Adaboost (Y. Freund & R. Schapire, Machine Learning: Proceedings of the Thirteenth International conference, aaa, 148–156), but are more robust with respect to noise. Internal estimates monitor error, strength, and correlation and these are used to show the response to increasing the number of features used in the splitting. Internal estimates are also used to measure variable importance. These ideas are also applicable to regression.

79,257 citations


"Soil microbial communities drive th..." refers methods in this paper

  • ...Random Forest modelling To gain a mechanistic understanding of the drivers of MRGC, we conducted a classification Random Forest analysis (Breiman 2001) as described in Delgado-Baquerizo et al....

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  • ...To gain a mechanistic understanding of the drivers of MRGC, we conducted a classification Random Forest analysis (Breiman 2001) as described in Delgado-Baquerizo et al. (2016), which allowed us to identify common microbial predictors across sites....

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01 Jan 2003
TL;DR: Some guidelines that should help applied researchers to evaluate the adequacy of a given structural equation model are provided.
Abstract: For structural equation models, a huge variety of fit indices has been developed. These indices, however, can point to conflicting conclusions about the extent to which a model actually matches the observed data. The present article provides some guidelines that should help applied researchers to evaluate the adequacy of a given structural equation model. First, as goodness-of-fit measures depend on the method used for parameter estimation, maximum likelihood (ML) and weighted least squares (WLS) methods are introduced in the context of structural equation modeling. Then, the most common goodness-of-fit indices are discussed and some recommendations for practitioners given. Finally, we generated an artificial data set according to a "true" model and analyzed two misspecified and two correctly specified models as examples of poor model fit, adequate fit, and good fit.

6,539 citations


"Soil microbial communities drive th..." refers background or methods in this paper

  • ...00) (Schermelleh-Engel et al. 2003) and (3) Bollen–Stine bootstrap test (the model has a good fit when 0....

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  • ...00) (Schermelleh-Engel et al. 2003), (2) The root mean square error of approximation (RMSEA; the model has a good fit when 0 ≤ RMSEA ≤ 0....

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  • ...There is no single universally accepted test of overall goodness-of-fit for SEM (Schermelleh-Engel et al. 2003)....

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  • ...…three metrics to quantify the goodness of fit of our model: (1) Chi-square test (v2; the model has a good fit when 0 ≤ v2/df ≤ 2 and 0.05 < P ≤ 1.00) (Schermelleh-Engel et al. 2003), (2) The root mean square error of approximation (RMSEA; the model has a good fit when 0 ≤ RMSEA ≤ 0.05 and 0.10…...

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  • ...…(Schermelleh-Engel et al. 2003), (2) The root mean square error of approximation (RMSEA; the model has a good fit when 0 ≤ RMSEA ≤ 0.05 and 0.10 < P ≤ 1.00) (Schermelleh-Engel et al. 2003) and (3) Bollen–Stine bootstrap test (the model has a good fit when 0.10 < Bollen–Stine bootstrap Pvalue ≤…...

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Journal ArticleDOI
TL;DR: Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in this study.
Abstract: For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r(2) = 0.70 and r(2) = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms.

4,376 citations


"Soil microbial communities drive th..." refers background in this paper

  • ...Soil microbes are the most abundant and diverse organisms on Earth (Fierer & Jackson 2006; Locey & Lennon 2016)....

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  • ...In the short-term – while improvements in microbial isolation and culturing techniques take place, our results suggest that MRCG could be promoted by altering soil properties such as pH, a major driver of microbial community composition (Fierer & Jackson 2006; Lauber et al. 2009)....

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  • ...Aridity and soil properties such as total organic carbon and pH are major drivers of microbial community composition in drylands (Fierer & Jackson 2006; Fierer et al. 2012; Maestre et al. 2015)....

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  • ...Furthermore, little is known about how changes in the composition of microbial communities 1Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA 2Departamento de Biolog ıa, Geolog ıa, F ısica y Qu ımica Inorg anica, Escuela Superior de Ciencias Experimentales y Tecnolog ıa, Universidad Rey Juan Carlos, c/ Tulip an s/n 28933, M ostoles, Spain 3Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia 4Hawkesbury Institute for the Environment, Western Sydney University, Penrith 2751, NSW, Australia 5Global Centre for Land Based Innovation, University of Western Sydney, Building L9, Locked Bag 1797, Penrith South, NSW 2751, Australia *Correspondence: E-mail: m.delgadobaquerizo@gmail.com © 2017 John Wiley & Sons Ltd/CNRS across such scales (e.g. dissimilarity across sites; b-diversity) affect MRGC, particularly in drylands....

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  • ...The importance of soil pH as a major driver of the composition of bacterial and fungal communities in terrestrial ecosystems is well known (Fierer & Jackson 2006; Lauber et al. 2009)....

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Book
24 Mar 2014

3,964 citations


"Soil microbial communities drive th..." refers background in this paper

  • ...This temperature increase mimics global warming forecasts by the end of this century (A2 scenario from IPCC 2013)....

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Journal ArticleDOI
01 Jun 2007-Ecology
TL;DR: Survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals.
Abstract: Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information in an ecological context, including which groups of bacteria are most abundant in different soils and why. With this study, we examined how the abundances of major soil bacterial phyla correspond to the biotic and abiotic characteristics of the soil environment to determine if they can be divided into ecologically meaningful categories. To do this, we collected 71 unique soil samples from a wide range of ecosystems across North America and looked for relationships between soil properties and the relative abundances of six dominant bacterial phyla (Acidobacteria, Bacteroidetes, Firmicutes, Actinobacteria, alpha-Proteobacteria, and the beta-Proteobacteria). Of the soil properties measured, net carbon (C) mineralization rate (an index of C availability) was the best predictor of phylum-level abundances. There was a negative correlation between Acidobacteria abundance and C mineralization rates (r2 = 0.26, P < 0.001), while the abundances of beta-Proteobacteria and Bacteroidetes were positively correlated with C mineralization rates (r2 = 0.35, P < 0.001 and r2 = 0.34, P < 0.001, respectively). These patterns were explored further using both experimental and meta-analytical approaches. We amended soil cores from a specific site with varying levels of sucrose over a 12-month period to maintain a gradient of elevated C availabilities. This experiment confirmed our survey results: there was a negative relationship between C amendment level and the abundance of Acidobacteria (r2 = 0.42, P < 0.01) and a positive relationship for both Bacteroidetes and beta-Proteobacteria (r2 = 0.38 and 0.70, respectively; P < 0.01 for each). Further support for a relationship between the relative abundances of these bacterial phyla and C availability was garnered from an analysis of published bacterial clone libraries from bulk and rhizosphere soils. Together our survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals. By applying the copiotroph-oligotroph concept to soil microorganisms we can make specific predictions about the ecological attributes of various bacterial taxa and better understand the structure and function of soil bacterial communities.

3,423 citations


"Soil microbial communities drive th..." refers background or result in this paper

  • ...…in these analyses for two main reasons (1) information on microbial functional traits has become increasingly available at this taxonomic level (Fierer et al. 2007; Trivedi et al. 2013); and (2) unlike high taxonomic rank information (OTU/genus), classlevel taxa are shared across all soil…...

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  • ...The positive effect of Solibacteres on the resistance of labile C mineralisation is consistent with results from previous studies suggesting that oligotrophic communities (sensu Fierer et al. 2007; Trivedi et al. 2013) promote the resistance of functions related to C cycle (de Vries & Shade 2013)....

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  • ...For example the relative abundance of class Saprospirae (Bacteroidetes), classified as rstrategist or copiotrophs (Fierer et al. 2007) directly and negatively affected multifunctionality resistance and labile C availability resistance to warming, presumably due to their rapid growth....

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