Search

Anthropogenic nitrogen (N) loading alters soil ammonia‐oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize 68 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N‐stimulation of nitrification, but does so via climate‐related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N‐availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate‐related shifts in soil ammonia‐oxidizing community maintain the N‐stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading. [ABSTRACT FROM AUTHOR]

Antibiotic resistance is one of the greatest public health challenges of our time. International efforts to curb resistance have largely focused on drug development and limiting unnecessary antibiotic use. However, in areas where water, sanitation, and hygiene infrastructure is lacking, we propose that bacterial flow between humans and animals can exacerbate the emergence and spread of resistant pathogens. Here, we describe the consequences of poor environmental controls by comparing mobile resistance elements among Escherichia coli recovered from humans and meat in Cambodia, a middle‐income country with substantial human–animal connectivity and unregulated antibiotic use. We identified identical mobile resistance elements and a conserved transposon region that were widely dispersed in both humans and animals, a phenomenon rarely observed in high‐income settings. Our findings indicate that plugging leaks at human–animal interfaces should be a critical part of addressing antibiotic resistance in low‐ and especially middle‐income countries. [ABSTRACT FROM AUTHOR]

Quantitatively summarizing results from a collection of primary studies with meta-analysis can help answer ecological questions and identify knowledge gaps. The accuracy of the answers depends on the quality of the meta-analysis. We reviewed the literature assessing the quality of ecological meta-analyses to evaluate current practices and highlight areas that need improvement. From each of the 18 review papers that evaluated the quality of meta-analyses, we calculated the percentage of meta-analyses that met criteria related to specific steps taken in the meta-analysis process (i.e., execution) and the clarity with which those steps were articulated (i.e., reporting). We also re-evaluated all the meta-analyses available from Pappalardo et al. [1] to extract new information on ten additional criteria and to assess how the meta-analyses recognized and addressed non-independence. In general, we observed better performance for criteria related to reporting than for criteria related to execution; however, there was a wide variation among criteria and meta-analyses. Meta-analyses had low compliance with regard to correcting for phylogenetic non-independence, exploring temporal trends in effect sizes, and conducting a multifactorial analysis of moderators (i.e., explanatory variables). In addition, although most meta-analyses included multiple effect sizes per study, only 66% acknowledged some type of non-independence. The types of non-independence reported were most often related to the design of the original experiment (e.g., the use of a shared control) than to other sources (e.g., phylogeny). We suggest that providing specific training and encouraging authors to follow the PRISMA EcoEvo checklist recently developed by O'Dea et al. [2] can improve the quality of ecological meta-analyses. [ABSTRACT FROM AUTHOR]

Global climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere‐climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2. Collectively, we demonstrate that long‐term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere‐climate feedback in Mediterranean‐type water‐limited ecosystems, namely how eP induces soil C loss via microbe‐plant–soil interplay. [ABSTRACT FROM AUTHOR]

Soils store more carbon than other terrestrial ecosystems1,2. How soil organic carbon (SOC) forms and persists remains uncertain1,3, which makes it challenging to understand how it will respond to climatic change3,4. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss5–7. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways4,6,8–11, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes12,13. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved7,14,15. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.A deep learning and data-driven modelling study finds that microbial carbon use efficiency is a major determinant of soil organic carbon storage and its spatial variation across the globe. [ABSTRACT FROM AUTHOR]

Density dependence in an ecological community has been observed in many macro-organismal ecosystems and is hypothesized to maintain biodiversity but is poorly understood in microbial ecosystems. Here, we analyze data from an experiment using quantitative stable isotope probing (qSIP) to estimate per-capita growth and mortality rates of bacterial populations in soils from several ecosystems along an elevation gradient which were subject to nutrient addition of either carbon alone (glucose; C) or carbon with nitrogen (glucose + ammonium-sulfate; C + N). Across all ecosystems, we found that higher population densities, quantified by the abundance of genomes per gram of soil, had lower per-capita growth rates in C + N-amended soils. Similarly, bacterial mortality rates in C + N-amended soils increased at a significantly higher rate with increasing population size than mortality rates in control and C-amended soils. In contrast to the hypothesis that density dependence would promote or maintain diversity, we observed significantly lower bacterial diversity in soils with stronger negative density-dependent growth. Here, density dependence was significantly but weakly responsive to nutrients and was not associated with higher bacterial diversity. [ABSTRACT FROM AUTHOR]

Background: Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m−2 year−1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century. Results: Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition. Conclusions: We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation. 746vo4z91jPxc1uFvBMbFc Video Abstract [ABSTRACT FROM AUTHOR]

Scope: Biochemistry is an essential yet undervalued aspect of soil ecology, especially when analyzing soil C cycling. We assume, based on tradition, intuition or hope, that the complexity of biochemistry is confined to the microscopic world, and can be ignored when dealing with whole soil systems. This opinion paper draws attention to patterns caused by basic biochemical processes that permeate the world of ecosystem processes. From these patterns, we can estimate activities of the biochemical reactions of the central C metabolic network and gain insights into the ecophysiology of microbial biosynthesis, growth, and maintenance energy requirements: important components of Carbon Use Efficiency (CUE). Observations: We show that glucose is processed via the Embden-Meyerhof-Parnas glycolysis in one soil, but via Pentose Phosphate or Entner-Doudoroff pathways in two other soils. However, notwithstanding this metabolic diversity, glucose use efficiency is high and thus substrate use for maintenance energy and overflow respiration is low in these soils. These results contradict current dogma, based on four decades of debate in soil ecology, that the maintenance energy demand in soil communities is a quantitative important, although variable, component of soil community energy metabolism. Conclusions: We identify three main shortcomings in our current understanding of substrate use efficiency: 1) in numeric and conceptual models, we lack appreciation of the strategies that microbes employ to quickly reduce energy needs in response to starvation; 2) in order to understand variation in CUE, we need to improve our understanding of the processes of exudation (including all changes in allocation of C from the cell soluble to insoluble fraction and extracellular environment) and microbial turnover; and 3) whether tracer experiments can be used to measure the long-term substrate use efficiency of soil microbial communities depends critically on the ability and speed with which non-growing cells take up tracer substrates and metabolism activates and subsequently de-activates in response to starvation, as well as on how cellular activities scale to the community level. To move the field of soil ecology forward, future research must consider the details of microbial ecophysiology and develop new tools that enable direct measurement of microbial functioning in intact soils. We submit that 13C metabolic flux analysis is one of those new tools. [ABSTRACT FROM AUTHOR]

Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N2O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N‐induced changes in soil N2O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N2O emission by 261%, whereas there was no clear relationship between changes in soil N2O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field‐based results challenge the laboratory‐based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N2O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N‐induced changes in soil N2O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N2O emission. [ABSTRACT FROM AUTHOR]

Aim: Climate warming and biodiversity loss both alter plant productivity, yet we lack an understanding of how biodiversity regulates the responses of ecosystems to warming. In this study, we examine how plant diversity regulates the responses of grassland productivity to experimental warming using meta‐analytic techniques. Location: Global. Major taxa studied: Grassland ecosystems. Methods: Our meta‐analysis is based on warming responses of 40 different plant communities obtained from 20 independent studies on grasslands across five continents. Results: Our results show that plant diversity and its responses to warming were the most important factors regulating the warming effects on plant productivity, among all the factors considered (plant diversity, climate and experimental settings). Specifically, warming increased plant productivity when plant diversity (indicated by effective number of species) in grasslands was lower than 10, whereas warming decreased plant productivity when plant diversity was greater than 10. Moreover, the structural equation modelling showed that the magnitude of warming enhanced plant productivity by increasing the performance of dominant plant species in grasslands of diversity lower than 10. The negative effects of warming on productivity in grasslands with plant diversity greater than 10 were partly explained by diversity‐induced decline in plant dominance. Main conclusions: Our findings suggest that the positive or negative effect of warming on grassland productivity depends on how biodiverse a grassland is. This may mainly be due to differences in how warming may affect plant dominance and subsequent shifts in interspecific interactions in grasslands of different plant diversity levels. [ABSTRACT FROM AUTHOR]

The carbon stored in soil exceeds that of plant biomass and atmospheric carbon and its stability can impact global climate. Growth of decomposer microorganisms mediates both the accrual and loss of soil carbon. Growth is sensitive to temperature and given the vast biological diversity of soil microorganisms, the response of decomposer growth rates to warming may be strongly idiosyncratic, varying among taxa, making ecosystem predictions difficult. Here, we show that 15 years of warming by transplanting plant–soil mesocosms down in elevation, strongly reduced the growth rates of soil microorganisms, measured in the field using undisturbed soil. The magnitude of the response to warming varied among microbial taxa. However, the direction of the response—reduced growth—was universal and warming explained twofold more variation than did the sum of taxonomic identity and its interaction with warming. For this ecosystem, most of the growth responses to warming could be explained without taxon‐specific information, suggesting that in some cases microbial responses measured in aggregate may be adequate for climate modeling. Long‐term experimental warming also reduced soil carbon content, likely a consequence of a warming‐induced increase in decomposition, as warming‐induced changes in plant productivity were negligible. The loss of soil carbon and decreased microbial biomass with warming may explain the reduced growth of the microbial community, more than the direct effects of temperature on growth. These findings show that direct and indirect effects of long‐term warming can reduce growth rates of soil microbes, which may have important feedbacks to global warming. [ABSTRACT FROM AUTHOR]

Summary: Soils are among the most biodiverse habitats on earth and while the species composition of microbial communities can influence decomposition rates and pathways, the functional significance of many microbial species and phylogenetic groups remains unknown. If bacteria exhibit phylogenetic organization in their function, this could enable ecologically meaningful classification of bacterial clades. Here, we show non‐random phylogenetic organization in the rates of relative carbon assimilation for both rapidly mineralized substrates (amino acids and glucose) assimilated by many microbial taxa and slowly mineralized substrates (lipids and cellulose) assimilated by relatively few microbial taxa. When mapped onto bacterial phylogeny using ancestral character estimation this phylogenetic organization enabled the identification of clades involved in the decomposition of specific soil organic matter substrates. Phylogenetic organization in substrate assimilation could provide a basis for predicting the functional attributes of uncharacterized microbial taxa and understanding the significance of microbial community composition for soil organic matter decomposition. [ABSTRACT FROM AUTHOR]

Nutrient amendment diminished bacterial functional diversity, consolidating carbon flow through fewer bacterial taxa. Here, we show strong differences in the bacterial taxa responsible for respiration from four ecosystems, indicating the potential for taxon-specific control over soil carbon cycling. Trends in functional diversity, defined as the richness of bacteria contributing to carbon flux and their equitability of carbon use, paralleled trends in taxonomic diversity although functional diversity was lower overall. Among genera common to all ecosystems, Bradyrhizobium, the Acidobacteria genus RB41, and Streptomyces together composed 45–57% of carbon flow through bacterial productivity and respiration. Bacteria that utilized the most carbon amendment (glucose) were also those that utilized the most native soil carbon, suggesting that the behavior of key soil taxa may influence carbon balance. Mapping carbon flow through different microbial taxa as demonstrated here is crucial in developing taxon-sensitive soil carbon models that may reduce the uncertainty in climate change projections. The fate of soil carbon depends on microbial processes, but whether different microbial taxa have individualistic effects on carbon fluxes is unknown. Here the authors use 16 S amplicon sequencing and stable isotopes to show how taxonomic differences influence bacterial respiration and carbon cycling across four ecosystems. [ABSTRACT FROM AUTHOR]

Despite abounding evidence that leaf litter traits can predict decomposition rate, the way these traits influence trophic efficiency and element transfer to higher trophic levels is not resolved. Here, we used litter labeled with 13C and 15N stable isotopes to trace fluxes of litter C and N from four leaf types to freshwater invertebrate communities. We measured absolute (mg C or N) and relative assimilation (percentage of litter C or N incorporated into invertebrate biomass relative to C and N lost during decomposition). Four patterns emerged: (1) Invertebrate communities assimilated more C and N from slowly decomposing litter than communities feeding on rapidly decomposing litter; (2) absolute assimilation of both C and N in leaf packs was positively correlated with the relative biomass of invertebrate taxa in leaf packs; (3) Chironomidae larvae, which colonize packs in the early decomposition stages, assimilated the most C and N by the end of the 35-day experiment; and (4) most taxa, spanning five functional feeding groups (collector–gatherers, shredders, collector–filterers, scrapers, and predators), showed similar patterns in both absolute and relative assimilation across leaf types. These results challenge traditional views of litter quality by demonstrating that trophic efficiency is negatively associated with decomposition rate across these four leaf types. [ABSTRACT FROM AUTHOR]

Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these traits to detect relationships between microbial communities and ecosystem-scale properties, few studies have assessed these traits on a community-scale. Here, we analysed these traits from publicly available metagenomes derived from marine, soil, host-associated and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, consistent with genomic streamlining, with GC content in thermophilic communities generally higher than in marine systems. In contrast, soil communities averaging smaller genomes featured higher GC content and were often from low-carbon environments, suggesting unique selection pressures in soil bacteria. The abundance of specific σ-factors varied with average genome size and ecosystem type. In oceans, abundance of fliA, a σ-factor controlling flagella biosynthesis, was positively correlated with community average genome size--reflecting known trade-offs between nutrient conservation and chemotaxis. In soils, a high abundance of the stress response σ-factor gene rpoS was associated with smaller average genome size and often located in harsh and/or carbon-limited environments--a result which tracks features observed in culture and indicates an increased capacity for stress response in nutrient-poor soils. This work shows how ecosystem-specific constraints are associated with trade-offs which are embedded in the genomic features of bacteria in microbial communities, and which can be detected at the community level, highlighting the importance of genomic features in microbial community analysis. [ABSTRACT FROM AUTHOR]

Copyright of Methods in Ecology & Evolution is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background and aims: Through agriculture and industry, humans are increasing the deposition and availability of nitrogen (N) in ecosystems worldwide. Carbon (C) isotope tracers provide useful insights into soil C dynamics, as they allow to study soil C pools of different ages. We evaluated to what extent N enrichment affects soil C dynamics in experiments that applied C isotope tracers. Methods: Using meta-analysis, we synthesized data from 35 published papers. We made a distinction between "new C" and "old C" stocks, i.e., soil C derived from plant C input since the start of the isotopic enrichment, or unlabeled, pre-existing soil C. Results: Averaged across studies, N addition increased new soil C stocks (+30.3%), total soil C stocks (+6.1%) and soil C input proxies (+30.7%). Although N addition had no overall, average, effect on old soil C stocks and old soil C respiration, old soil C stocks increased with the amount of N added and respiration of old soil C declined. Nitrogen-induced effects on new soil C and soil C input both decreased with the amount of extraneous N added in control treatments. Conclusion: Although our findings require additional confirmation from long-term field experiments, our analysis provides isotopic evidence that N addition stimulates soil C storage both by increasing soil C input and (at high N rates) by decreasing decomposition of old soil C. Furthermore, we demonstrate that the widely reported saturating response of plant growth to N enrichment also applies to new soil C storage. [ABSTRACT FROM AUTHOR]

Increased human‐derived nitrogen (N) deposition to terrestrial ecosystems has resulted in widespread phosphorus (P) limitation of net primary productivity. However, it remains unclear if and how N‐induced P limitation varies over time. Soil extracellular phosphatases catalyze the hydrolysis of P from soil organic matter, an important adaptive mechanism for ecosystems to cope with N‐induced P limitation. Here we show, using a meta‐analysis of 140 studies and 668 observations worldwide, that N stimulation of soil phosphatase activity diminishes over time. Whereas short‐term N loading (≤5 years) significantly increased soil phosphatase activity by 28%, long‐term N loading had no significant effect. Nitrogen loading did not affect soil available P and total P content in either short‐ or long‐term studies. Together, these results suggest that N‐induced P limitation in ecosystems is alleviated in the long‐term through the initial stimulation of soil phosphatase activity, thereby securing P supply to support plant growth. Our results suggest that increases in terrestrial carbon uptake due to ongoing anthropogenic N loading may be greater than previously thought. [ABSTRACT FROM AUTHOR]

Microorganisms in soil assimilate, transform, and mineralize soil C to support growth. There are an estimated 2.6 × 1029 microbial cells containing 26 Pg C in soils worldwide. Consequently, quantifying microbial growth in soil is critical for determining the degree to which microorganisms contribute to the global C cycle. Measuring taxonspecific microbial growth enables understanding of the contribution of microbial taxa to elemental transformations across ecosystems and their susceptibility to environmental perturbations. These measurements in soil have largely been lacking due to inadequate methods. Quantitative stable isotope probing (qSIP) with H218O is used to measure taxon‐specific growth of microbial taxa in soil, an improvement compared with traditional stable isotope probing (SIP). In qSIP, DNA extracted from both a labeled (18O‐enriched water) and an unlabeled treatment is separated into numerous density fractions by isopycnic centrifugation, and target genes are quantified and sequenced in each fraction. The taxon‐specific DNA density shift and ultimately the isotopic composition (18O enrichment) is calculated for each taxon. Here we discuss methods and illustrate the procedure for quantifying microbial taxon‐specific growth in soil with qSIP using heavy isotope enriched H218O. [ABSTRACT FROM AUTHOR]

Elevated atmospheric CO2 (eCO2) generally increases carbon input in rice paddy soils and stimulates the growth of methane‐producing microorganisms. Therefore, eCO2 is widely expected to increase methane (CH4) emissions from rice agriculture, a major source of anthropogenic CH4. Agricultural practices strongly affect CH4 emissions from rice paddies as well, but whether these practices modulate effects of eCO2 is unclear. Here we show, by combining a series of experiments and meta‐analyses, that whereas eCO2 strongly increased CH4 emissions from paddies without straw incorporation, it tended to reduce CH4 emissions from paddy soils with straw incorporation. Our experiments also identified the microbial processes underlying these results: eCO2 increased methane‐consuming microorganisms more strongly in soils with straw incorporation than in soils without straw, with the opposite pattern for methane‐producing microorganisms. Accounting for the interaction between CO2 and straw management, we estimate that eCO2 increases global CH4 emissions from rice paddies by 3.7%, an order of magnitude lower than previous estimates. Our results suggest that the effect of eCO2 on CH4 emissions from rice paddies is smaller than previously thought and underline the need for judicious agricultural management to curb future CH4 emissions. [ABSTRACT FROM AUTHOR]

Climate warming affects soil carbon (C) dynamics, with possible serious consequences for soil C stocks and atmospheric CO2 concentrations. However, the mechanisms underlying changes in soil C storage are not well understood, hampering long‐term predictions of climate C‐feedbacks. The activity of the extracellular enzymes ligninase and cellulase can be used to track changes in the predominant C sources of soil microbes and can thus provide mechanistic insights into soil C loss pathways. Here we show, using meta‐analysis, that reductions in soil C stocks with warming are associated with increased ratios of ligninase to cellulase activity. Furthermore, whereas long‐term (≥5 years) warming reduced the soil recalcitrant C pool by 14%, short‐term warming had no significant effect. Together, these results suggest that warming stimulates microbial utilization of recalcitrant C pools, possibly exacerbating long‐term climate‐C feedbacks. [ABSTRACT FROM AUTHOR]

Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies have focused on how fire affects taxonomic and functional diversities of soil microbial communities, along with changes in plant communities and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects in a grassland ecosystem 9 months after an experimental fire at the Jasper Ridge Global Change Experiment site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis showing that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa was able to withstand the disturbance. In addition, fire decreased the relative abundances of most functional genes associated with C degradation and N cycling, implicating a slowdown of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated above‐ and belowground plant growth, likely enhancing plant–microbe competition for soil inorganic N, which was reduced by a factor of about 2. To synthesize those findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for significantly higher soil respiration rates in burned sites. Together, our results demonstrate that fire ‘reboots’ the grassland ecosystem by differentially regulating plant and soil microbial communities, leading to significant changes in soil C and N dynamics.Fire significantly increased environmental selection pressure on soil microbial community, where a small subset of highly connected taxa was able to withstand the disturbance. Fire decreased the relative abundances of most functional genes associated with C degradation and N cycling, but stimulated above‐ and belowground plant growth, likely enhancing plant–microbe competition for soil inorganic N. Plants but not microbial communities were responsible for significantly higher soil respiration rates in burned sites. [ABSTRACT FROM AUTHOR]

Rice is a staple food for nearly half of the world's population, but rice paddies constitute a major source of anthropogenic CH4 emissions. Root exudates from growing rice plants are an important substrate for methane‐producing microorganisms. Therefore, breeding efforts optimizing rice plant photosynthate allocation to grains, i.e., increasing harvest index (HI), are widely expected to reduce CH4 emissions with higher yield. Here we show, by combining a series of experiments, meta‐analyses and an expert survey, that the potential of CH4 mitigation from rice paddies through HI improvement is in fact small. Whereas HI improvement reduced CH4 emissions under continuously flooded (CF) irrigation, it did not affect CH4 emissions in systems with intermittent irrigation (II). We estimate that future plant breeding efforts aimed at HI improvement to the theoretical maximum value will reduce CH4 emissions in CF systems by 4.4%. However, CF systems currently make up only a small fraction of the total rice growing area (i.e., 27% of the Chinese rice paddy area). Thus, to achieve substantial CH4 mitigation from rice agriculture, alternative plant breeding strategies may be needed, along with alternative management. Breeding efforts optimizing photosynthate allocation to grains, i.e., increasing harvest index (HI), are widely expected to reduce CH4 emissions from rice cultivation. Here we show, by combining a series of experiments, meta‐analyses, and an expert assessment, that the potential of CH4 mitigation from rice paddies through HI improvement is actually small. We estimate that future HI improvement will reduce CH4 emissions in continuously flooded systems (CF) by 4.4% at most. Furthermore, HI improvement did not affect CH4 emissions in systems with intermittent irrigation (II); these systems make up a large part of the China's rice growing area and are becoming increasingly popular. [ABSTRACT FROM AUTHOR]

Plant diversity can increase biomass production in plot‐scale studies, but applying these results to ecosystem carbon (C) storage at larger spatial and temporal scales remains problematic. Other ecosystem controls interact with diversity and plant production, and may influence soil pools differently from plant pools. We integrated diversity with the state‐factor framework, which identifies key controls, or 'state factors', over ecosystem properties and services such as C storage. We used this framework to assess the effects of diversity, plant traits and state factors (climate, topography, time) on live tree, standing dead, organic horizon and total C in Québec forests. Four patterns emerged: (1) while state factors were usually the most important model predictors, models with both state and biotic factors (mean plant traits and diversity) better predicted C pools; (2) mean plant traits were better predictors than diversity; (3) diversity increased live tree C but reduced organic horizon C; (4) different C pools responded to different traits and diversity metrics. These results suggest that, where ecosystem properties result from multiple processes, no simple relationship may exist with any one organismal factor. Integrating biodiversity into ecosystem ecology and assessing both traits and diversity improves our mechanistic understanding of biotic effects on ecosystems. [ABSTRACT FROM AUTHOR]

Abstract: Heat waves are increasing in frequency and intensity, presenting a challenge for the already difficult practice of ecological restoration. We investigated whether pre‐heating locally sourced rhizosphere soil (inoculum) could acclimatize plants to a field‐imposed heat wave in a restoration setting. Soil heating in the laboratory caused a marked shift in rhizosphere bacterial community composition, accompanied by an increase in species evenness. Furthermore, pre‐heated rhizosphere soil reduced plant height, number of leaves, and shoot mass of the C4 grass, blue grama (Bouteloua gracilis), and it reduced the shoot mass of the C3 grass, Arizona fescue (Festuca arizonica) in the glasshouse. Following transplantation and the application of a field heat wave, pre‐heated inoculum did not influence heat wave survival for either plant species. However, there were strong species‐level responses to the field heat wave. For instance, heat wave survivorship was over four times higher in blue grama (92%) than in Arizona fescue (22%). These results suggest that the use of C4 seeds may be preferable for sites exhibiting high heat wave risk. Further research is needed to understand whether inocula are more effective in highly degraded soil in comparison with partially degraded soils. [ABSTRACT FROM AUTHOR]

Abstract: Leaf litter provides an important nutrient subsidy to headwater streams, but little is known about how tree genetics influence energy pathways from litter to higher trophic levels. Despite the charge to quantify carbon (C) and nitrogen (N) pathways from decomposing litter, the relationship between litter decomposition and aquatic consumers remains unresolved. We measured litter preference (attachments to litter), C and N assimilation rates, and growth rates of a shredding caddisfly (Hesperophylax magnus, Limnephilidae) in response to leaf litter of different chemical and physical phenotypes using Populus cross types (P. fremontii, P. angustifolia, and F1 hybrids) and genotypes within P. angustifolia. We combined laboratory mesocosm studies using litter from a common garden with a field study using doubly labeled litter (13C and 15N) grown in a greenhouse and incubated in Oak Creek, Arizona, USA. We found that, in the lab, shredders initially chose relatively labile (low lignin and condensed tannin concentrations, rapidly decomposing) cross type litter, but preference changed within 4 d to relatively recalcitrant (high lignin and condensed tannin concentrations, slowly decomposing) litter types. Additionally, in the lab, shredder growth rates were higher on relatively recalcitrant compared to labile cross type litter. Over the course of a three‐week field experiment, shredders also assimilated more C and N from relatively recalcitrant compared to labile cross type litter. Finally, among P. angustifolia genotypes, N assimilation by shredders was positively related to litter lignin and C:N, but negatively related to condensed tannins and decomposition rate. C assimilation was likewise positively related to litter C:N, and also to litter %N. C assimilation was not associated with condensed tannins or lignin. Collectively, these findings suggest that relatively recalcitrant litter of Populus cross types provides more nutritional benefit, in terms of N fluxes and growth, than labile litter, but among P. angustifolia genotypes the specific trait of litter recalcitrance (lignin or tannins) determines effects on C or N assimilation. As shredders provide nutrients and energy to higher trophic levels, the influence of these genetically based plant decomposition pathways on shredder preference and performance may affect community and food web structure. [ABSTRACT FROM AUTHOR]

Abstract: Dams disrupt the river continuum, altering hydrology, biodiversity and energy flow. Although research indicates that tributary inputs have the potential to dilute these effects, knowledge at the food‐web level is still scarce. Here, we examined the riverine food‐web structure of the Colorado River below Glen Canyon Dam, focusing on organic matter sources, trophic diversity and food chain length. We asked how these components respond to pulsed flows from tributaries following monsoon thunderstorms that seasonally increase streamflow in the American Southwest. Tributaries increased the relative importance of terrestrial organic matter, particularly during the wet season below junctures of key tributaries. This contrasted with the algal‐based food‐web present immediately below Glen Canyon Dam. Tributary inputs during the monsoon also increased trophic diversity and food chain length: food chain length peaked below the confluence with the largest tributary (by discharge) in Grand Canyon, increasing by >1 trophic level over a 4–5 km reach possibly due to aquatic prey being flushed into the mainstem during heavy rain events. Our results illustrate that large tributaries can create seasonal discontinuities, influencing riverine food‐web structure in terms of allochthony, food‐web diversity and food chain length. Synthesis and applications. Pulsed flows from unregulated tributaries following seasonal monsoon rains increase the importance of terrestrially derived organic matter in large, regulated river food webs, increasing food chain length and trophic diversity downstream of tributary inputs. Protecting unregulated tributaries within hydropower cascades may be important if we are to mitigate food‐web structure alteration due to flow regulation by large dams. This is critical in the light of global hydropower development, especially in megadiverse, developing countries where dam placement (including completed and planned structures) is in tributaries. [ABSTRACT FROM AUTHOR]

Ecologists often equate litter quality with decomposition rate. In soil and sediments, litter that is rapidly decomposed by microbes often has low concentrations of tannin and lignin and low C:N ratios. Do these same traits also favor element transfer to higher trophic levels in streams, where many insects depend on litter as their primary food source? We test the hypothesis that slow decomposition rates promote element transfer from litter to insects, whereas rapid decomposition favors microbes. We measured carbon and nitrogen fluxes from four plant species to a leaf-shredding caddisfly using isotopically labeled litter. Caddisflies assimilated a higher percentage of litter carbon and nitrogen lost from slowly decomposing litters (Platanus wrightii and Quercus gambelii). In contrast, rapidly decomposing litters (Fraxinus velutina and Populus fremontii) supported higher microbial biomass. These results challenge the view that rapidly decomposing litter is higher quality by demonstrating that slowly decomposing litters provide a critical resource for insects. [ABSTRACT FROM AUTHOR]

Classical niche partitioning theory posits increased competition for and partitioning of the most limiting resource among coexisting species. Coexisting plant species may vary in rooting depth, reflecting niche partitioning in water source use. Our goal was to assess the soil water partitioning of woody plant communities across northern Arizona along an elevational moisture gradient using stem and soil water isotopes from two sampling periods to estimate the use of different water sources. We hypothesized that niche overlap of water sources would be higher and monsoon precipitation uptake would be lower at sites with higher moisture availability. Pairwise niche overlap of coexisting species was calculated using mixing model estimates of proportional water use for three sources. Across the moisture gradient, niche overlap increased with site moisture index (precipitation/potential evapotranspiration) across seasons, and site moisture index explained 37% of the variation in niche overlap of intermediate and deeper sources of water. Desert trees utilized more winter source water than desert shrubs, suggesting the partitioning of water sources between functional groups. However, seasonal differences in surface water use were primarily found at intermediate levels of site moisture availability. Our findings support classical niche partitioning theory in that plants exhibit higher overlap of water sources when water is not a limiting resource. [ABSTRACT FROM AUTHOR]

Disruptions of natural flow impair rivers and streams worldwide. Those conducting restoration efforts have rarely explored how and when stream ecosystems can recover after reinstating natural flows. We quantified responses of ecosystem metabolism and N dynamics to the decommissioning and removal of a 100-y-old diversion dam in a desert stream, Fossil Creek, Arizona. Fossil Creek is a travertine river, meaning that CaCO3 concentrations in water in the springs that feed Fossil Creek are high enough to precipitate out of the water to form travertine terraces and deep pools. The majority of flow was diverted for power generation, so travertine deposition rates were significantly reduced and travertine terraces were smaller and less frequent compared to pre-dam historical records. Flow restoration enabled the recovery of the geochemical process of travertine deposition and increased gross primary production and N uptake to rates comparable to those measured in an upstream, reference reach. Reinstating a river’s natural flow regime can result in rapid and near-complete recovery of fundamental ecosystem processes that reshape the aquatic food web. [ABSTRACT FROM AUTHOR]

Summary: Nitrogen (N) is frequently a limiting nutrient in soil; its availability can govern ecosystem functions such as primary production and decomposition. Assimilation of N by microorganisms impacts the availability of N in soil. Despite its established ecological significance, the contributions of microbial taxa to N assimilation are unknown. Here we measure N uptake and use by microbial phylotypes and taxonomic groups within a diverse assemblage of soil microbes through quantitative stable isotope probing (qSIP) with 15N. Following incubation with 15 NH 4 +, distinct patterns of 15N assimilation among taxonomic groups were observed. For instance, glucose addition stimulated 15N assimilation in most members of Actinobacteria and Proteobacteria but generally decreased 15N use by Firmicutes and Bacteriodetes. While NH 4 + is considered a preferred and universal source of N to prokaryotes, the majority (> 80%) of N assimilation in our soils could be attributed to a handful of active orders. Characterizing N assimilation of taxonomic groups with 15N qSIP may provide a basis for understanding how microbial community composition influences N availability in the environment. [ABSTRACT FROM AUTHOR]

Leaf litter provides an important resource to forested stream ecosystems. During leaf fall a significant amount of dissolved organic carbon (DOC) enters streams as leaf leachate. We compared the effects of plant species and leaf leachate bioavailability on the composition of stream bacterial communities and rates of DOC decomposition. We used four common riparian tree species that varied in foliar chemistry, leachate optical properties, and litter decomposition rate. We used laboratory microcosms from two streams and amended with a standard concentration of DOC derived from leaf leachate of the four tree species. After 24 h, we measured rates of DOC biodegradation and determined the composition of the bacterial communities via bar-coded pyrosequencing of the 16S rRNA gene. The composition, diversity, and abundance of the bacterial community differed significantly among plant species from both streams. The phylogenetic distance of the different bacterial communities correlated with species-specific leachate optical properties and rates of DOC biodegradation. Highest rates of DOC decomposition were associated with high tannin and lignin leaf types. Results demonstrate that riparian plant species strongly influences stream bacterial communities via their leachate suggesting that alterations to the presence or abundance of riparian plant taxa may influence these communities and associated ecosystem processes. [ABSTRACT FROM AUTHOR]

Land ecosystems sequester on average about a quarter of anthropogenic CO2 emissions. It has been proposed that nitrogen (N) availability will exert an increasingly limiting effect on plants' ability to store additional carbon (C) under rising CO2, but these mechanisms are not well understood. Here, we review findings from elevated CO2 experiments using a plant economics framework, highlighting how ecosystem responses to elevated CO2 may depend on the costs and benefits of plant interactions with mycorrhizal fungi and symbiotic N-fixing microbes. We found that N-acquisition efficiency is positively correlated with leaf-level photosynthetic capacity and plant growth, and negatively with soil C storage. Plants that associate with ectomycorrhizal fungi and N-fixers may acquire N at a lower cost than plants associated with arbuscular mycorrhizal fungi. However, the additional growth in ectomycorrhizal plants is partly offset by decreases in soil C pools via priming. Collectively, our results indicate that predictive models aimed at quantifying C cycle feedbacks to global change may be improved by treating N as a resource that can be acquired by plants in exchange for energy, with different costs depending on plant interactions with microbial symbionts. [ABSTRACT FROM AUTHOR]

Breeding high-yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane ( CH4) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high-yielding rice cultivars actually reduce CH4 emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH4 emissions in a soil with a high carbon (C) content. Compared to a low-yielding cultivar, a high-yielding cultivar significantly increased root porosity and the abundance of methane-consuming microorganisms, suggesting that the larger and more porous root systems of high-yielding cultivars facilitated CH4 oxidation by promoting O2 transport to soils. Our results were further supported by a meta-analysis, showing that high-yielding rice cultivars strongly decrease CH4 emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH4 emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high-yielding cultivars can substantially mitigate paddy CH4 emission in China and other rice growing regions. [ABSTRACT FROM AUTHOR]

Rising levels of atmospheric CO2 frequently stimulate plant inputs to soil, but the consequences of these changes for soil carbon (C) dynamics are poorly understood. Plant-derived inputs can accumulate in the soil and become part of the soil C pool ('new soil C'), or accelerate losses of pre-existing ('old') soil C. The dynamics of the new and old pools will likely differ and alter the long-term fate of soil C, but these separate pools, which can be distinguished through isotopic labeling, have not been considered in past syntheses. Using meta-analysis, we found that while elevated CO2 (ranging from 550 to 800 parts per million by volume) stimulates the accumulation of new soil C in the short term (<1 year), these effects do not persist in the longer term (1-4 years). Elevated CO2 does not affect the decomposition or the size of the old soil C pool over either temporal scale. Our results are inconsistent with predictions of conventional soil C models and suggest that elevated CO2 might increase turnover rates of new soil C. Because increased turnover rates of new soil C limit the potential for additional soil C sequestration, the capacity of land ecosystems to slow the rise in atmospheric CO2 concentrations may be smaller than previously assumed. [ABSTRACT FROM AUTHOR]

The article discusses the ecological features that distinguish colonizing opportunistic pathogens (COP) from other bacterial pathogens. Topics covered include the public health implications arising from the unique biology of COP, the dynamics of COP among their human, animal, and environmental reservoirs that needed research, and the host immune response of COP and the mechanisms of how they transition from colonization to infection.

Antibiotic- resistant pathogens increasingly threaten human health. Widespread application of antibiotics to animal populations raised for food, including chickens, cattle, and pigs, selects for resistance and contributes to the evolution of those pathogens. Despite a half century of research establishing the mechanisms and pathways by which antibiotic- resistant bacteria spread from food animals to people, scientists lack the appropriate data and models to estimate the public health burden of antibiotic- resistant human infections attributable to antibiotic use in food- animal production. Genomic technologies are enabling researchers to track the bidirectional transmissions of specific bacterial strains from livestock to people -- and from people to livestock -- that can amplify resistance traits. Concepts in ecology, which were developed to understand resource subsidies, metapopulations, and biological invasions, provide insight into the epidemiology of antibiotic resistance from genomic data. By applying ecological principles to highly resolved phylogenetic data, researchers can improve strategies for controlling antibiotic resistance. [ABSTRACT FROM AUTHOR]

Background and aims: Plant growth promoting rhizobacteria (PGPR) have been shown to reduce abiotic stress on plants, but these effects have not been quantitatively synthesized. We evaluated the degree to which plant growth promoting rhizobacteria (PGPR) improve plant performance with and without drought stress. Methods: We used meta-analysis to summarize 52 published articles on the effects of PGPR on root mass, shoot mass and yield under well-watered and drought conditions. We also asked whether fertilization treatments, experimental conditions, inoculum taxonomic complexity, plant functional group, or inoculum delivery method introduce variation in the effect size of PGPR. Results: Across all treatments, plants were highly responsive to PGPR; under well-watered conditions, root mass increased by 35%, shoot mass increased by 28%, and reproductive yield increased by 19%. Under drought conditions, the effect was even higher: root mass increased by 43%, shoot mass increased by 45%, and reproductive yield increased by 40%. The effect of PGPR was significantly larger under drought for shoot mass ( p < 0.05) and reproductive yield ( p < 0.05), but not for root mass. PGPR responsiveness also varied according to plant functional group, with C grass shoot production responding the least strongly to PGPR. Conclusions: We demonstrate that PGPR are highly effective for improving plant growth, with a greater effect under drought for above ground traits. While previously known for their bio-control abilities, we show that PGPR may also contribute to drought amelioration and water conservation. [ABSTRACT FROM AUTHOR]

Species diversity affects the functioning of ecosystems, including the efficiency by which communities capture limited resources, produce biomass, recycle and retain biologically essential nutrients. These ecological functions ultimately support the ecosystem services upon which humanity depends. Despite hundreds of experimental tests of the effect of biodiversity on ecosystem function (BEF), it remains unclear whether diversity effects are sufficiently general that we can use a single relationship to quantitatively predict how changes in species richness alter an ecosystem function across trophic levels, ecosystems and ecological conditions. Our objective here is to determine whether a general relationship exists between biodiversity and standing biomass. We used hierarchical mixed effects models, based on a power function between species richness and biomass production (Y = a × Sb), and a database of 374 published experiments to estimate the BEF relationship (the change in biomass with the addition of species), and its associated uncertainty, in the context of environmental factors. We found that the mean relationship ( b = 0.26, 95% CI: 0.16, 0.37) characterized the vast majority of observations, was robust to differences in experimental design, and was independent of the range of species richness levels considered. However, the richness-biomass relationship varied by trophic level and among ecosystems; in aquatic systems b was nearly twice as large for consumers (herbivores and detritivores) compared to primary producers; in terrestrial ecosystems, b for detritivores was negative but depended on few studies. We estimated changes in biomass expected for a range of changes in species richness, highlighting that species loss has greater implications than species gains, skewing a distribution of biomass change relative to observed species richness change. When biomass provides a good proxy for processes that underpin ecosystem services, this relationship could be used as a step in modeling the production of ecosystem services and their dependence on biodiversity. [ABSTRACT FROM AUTHOR]

Identification of microorganisms that facilitate the cycling of nutrients in freshwater is paramount to understanding how these ecosystems function. Here, we identify growing aquatic bacteria using [ABSTRACT FROM AUTHOR]

The article highlights forest managers on stabilizing the forest carbon emission. Topics discussed include forest carbon stored by protecting carbon in soil and in large, old trees; small-tree carbon which is unstable and reason for shifting the natural disturbance from low to high intensity fire; and cost reduction in risk which provides a financial mechanism to stabilize forest carbon stores.

Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field experiment in a California grassland, we studied the main and interactive effects of three global change factors (increased atmospheric CO2 concentration, precipitation and nitrogen addition, and all their factorial combinations, based on global change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB). Using a trait-based model, we then tested whether categorizing NOB into a few functional groups unified by physiological traits enables understanding and predicting how soil NOB respond to global environmental change. Contrasted responses to global change treatments were observed between three main NOB functional types. In particular, putatively mixotrophic Nitrobacter, rare under most treatments, became dominant under the 'High CO2CNitrogenCPrecipitation' treatment. The mechanistic trait-based model, which simulated ecological niches of NOB types consistent with previous ecophysiological reports, helped predicting the observed effects of global change on NOB and elucidating the underlying biotic and abiotic controls. Our results are a starting point for representing the overwhelming diversity of soil bacteria by a few functional types that can be incorporated into models of terrestrial ecosystems and biogeochemical processes. [ABSTRACT FROM AUTHOR]