Belowground Microbial Communities Research Articles

Range-expansion effects on the belowground plant microbiome.

Plant range expansion is occurring at a rapid pace, largely in response to human-induced climate warming. While the movement of plants along latitudinal and altitudinal gradients is well documented, effects on the belowground microbial communities remains largely unknown. Further, in range expansion not all plant species are equal: in a new range the relatedness between range-expanding plant species and native flora can influence plant-microbe interactions. Here we used a latitudinal gradient across Europe to examine bacterial and fungal communities in the rhizosphere and surrounding soils of range-expanding plant species. We selected range expanders with and without congeneric natives in the new range, and as a control, the congeneric natives, totaling 382 plant individuals collected across Europe. In general, a plant’s status as range expander was a weak predictor of bacterial and fungal community composition. However, microbial communities of range-expanding plant species became more similar to each other farther from their original range. Range expanders unrelated to the native community also experienced a decrease in the ratio of plant pathogens to symbionts, giving weak support to the enemy release hypothesis. Even at a continental scale the effects of plant range expansion on the belowground microbiome are detectable, though changes to specific taxa remain difficult to decipher.

Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions.

Belowground microbial communities strongly influence ecosystem function such that predicting function may rely on understanding ecological processes that assemble communities. Uncertainty remains, however, in what governs the relative contributions of different ecological processes. To help fill this knowledge gap, we test the general hypothesis that both initial state and degree of change in environmental conditions govern the relative contributions of different ecological assembly processes. To do so, we leveraged regional-scale nutrient and organic matter addition experiments and used soil organic matter (SOM) as a proxy of integrated soil environmental conditions. Consistent with our hypothesis, we found that both the initial amount of SOM and the degree of change in SOM-in response to nutrient addition-influenced the relative contributions of different ecological assembly processes. These influences were most clearly observed at the regional scale, suggesting potential scale dependence. More specifically, nutrient additions homogenized bacterial community composition due to enhanced influences of homogenizing dispersal when SOM content was initially high. In contrast, nutrient additions led to divergence in community composition due to variable selection when initial SOM was low and/or when SOM increased significantly in response to nutrient additions. Our findings indicate important connections among initial conditions, degree of change in environmental variables and microbial community assembly processes that may influence ecosystem processes. These conceptual inferences highlight a need to strengthen connections between ecological theory and biogeochemical modelling.

Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage (Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory.

Rhizosphere microbial communities are known to be highly diverse and strongly dependent on various attributes of the host plant, such as species, nutritional status, and growth stage. High-throughput 16S rRNA gene amplicon sequencing has been used to characterize the rhizosphere bacterial community of many important crop species, but this is the first study to date to characterize the bacterial and archaeal community of Brassica oleracea var. capitata. The study also tested the response of the bacterial community to fertilizer type (organic or synthetic) and N dosage (high or low), in addition to plant age (9 or 12 weeks) and aphid (Myzus persicae) herbivory (present/absent). The impact of aboveground herbivory on belowground microbial communities has received little attention in the literature, and since the type (organic or mineral) and amount of fertilizer applications are known to affect M. percicae populations, these treatments were applied at agricultural rates to test for synergistic effects on the soil bacterial community. Fertilizer type and plant growth were found to result in significantly different rhizosphere bacterial communities, while there was no effect of aphid herbivory. Several operational taxonomic units were identified as varying significantly in abundance between the treatment groups and age cohorts. These included members of the S-oxidizing genus Thiobacillus, which was significantly more abundant in organically fertilized 12-week-old cabbages, and the N-fixing cyanobacteria Phormidium, which appeared to decline in synthetically fertilized soils relative to controls. These responses may be an effect of accumulating root-derived glucosinolates in the B. oleracea rhizosphere and increased N-availability, respectively.

Effects of Nitrogen and Phosphorus Inputs on Soil Bacterial Abundance, Diversity, and Community Composition in Chinese Fir Plantations.

Nutrient inputs to forest ecosystems significantly influence aboveground plant community structure and ecosystem functioning. However, our knowledge of the influence of nitrogen (N) and/or phosphorus (P) inputs on belowground microbial communities in subtropical forests is still unclear. In this study, we used quantitative polymerase chain reaction and Illumina Miseq sequencing of the bacterial 16S rRNA gene to investigate bacterial abundance, diversity, and community composition in a Chinese fir plantation. The fertilization regimes were as follows: untreated control (CK), P amendment (P), N amendment (N), and N with P amendment (NP). Additions of N decreased soil pH and bacterial 16S rRNA gene abundance by 3.95 (from 4.69 to 3.95) and 3.95 × 109 copies g−1 dry soil (from 9.27 × 109 to 3.95 × 109 g−1 dry soil), respectively. Bacterial richness and diversity decreased with N addition (N and NP) rather than only P input. Proteobacteria, Acidobacteria, and Actinobacteria were the major phylum across all treatments. Nitrogen addition increased the relative abundance of Proteobacteria and Actinobacteria by 42.0 and 10.5%, respectively, while it reduced that of Acidobacteria by 26.5%. Bacterial community structure in the CK and P treatments was different from that in the N and NP treatments upon principle coordinates analysis. Phosphorus addition did not significantly affect soil bacterial communities, and no interactions between N and P inputs on microbial traits were observed. Soil pH and mineral N availability appeared to have a cooperative effect on bacterial abundance and community structure, with soil pH being the key influencing factor by canonical correspondence analysis. These results indicate that inorganic N rather than P fertilization affected both bacterial abundance and community composition in subtropical forests.

Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass.

Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010–2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P < 0.05) increased root and microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P < 0.05) changed by clipping. Clipping significantly (P < 0.05) increased the abundances of labile carbon (C) degrading genes. More importantly, the abundances of recalcitrant C degrading genes were consistently and significantly (P < 0.05) increased by clipping in the last 2 years, which could accelerate recalcitrant C degradation and weaken long-term soil carbon stability. Furthermore, genes involved in nutrient-cycling processes including nitrogen cycling and phosphorus utilization were also significantly increased by clipping. The shifts of microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices.

Dynamics of soil microbial recovery from cropland to orchard along a 20-year chronosequence in a degraded karst ecosystem

The ‘Grain for Green’ project (GGP) is the largest ecological rehabilitation project in China. A large body of croplands has been abandoned or converted to shrubs or grasslands since 1999. Soil microbes are recognized as sensitive responders of environmental changes, therefore, they are considered as a key component of ecological rehabilitation. However, very limited field experiments have been conducted to investigate the responses of soil microorganisms to restoration projects, especially in karst regions of China. In order to evaluate the response of soil microbial community to ecological restoration, we determined soil microbial community composition by means of qPCR, PLFAs, and high-throughput amplicon sequencing following conversion of cropland to Chinese prickly ash (Zanthoxylum bungeanum Maxim) orchard (CP) along a 20-year chronosequence in a degraded karst ecosystem. Our results showed that soil nutrient contents significantly increased following cropland to CP conversion. qPCR results showed that the highest bacterial abundance was found in the 20-year CP, but bacterial abundance decreased during the first 5-year land-use conversion. Conversion of cropland to CP strongly impacted soil microbial community composition, despite the cropland sites having a long cultivation history (>50 years). However, soil bacterial diversity remained unchanged within a 20-year land-use conversion. Actinobacteria, Proteobacteria, and Acidobacteria were the main bacterial phyla in all land-use sites. In particular, various members of Actinobacteria (e.g., Solirubrobacteraceae) tended to increase their relative abundances in responding to land-use conversion, which may imply that the shifts of soil microbial communities associated with recovering of ecological conditions. Overall, given the rapid yet differential response to ecological restoration, investigation of the belowground microbial community can provide an effective way of assessing ecological recovery of restoration projects in the karst region.

Long‐term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro‐ecosystems across the globe

Long-term elevated nitrogen (N) input from anthropogenic sources may cause soil acidification and decrease crop yield, yet the response of the belowground microbial community to long-term N input alone or in combination with phosphorus (P) and potassium (K) is poorly understood. We explored the effect of long-term N and NPK fertilization on soil bacterial diversity and community composition using meta-analysis of a global dataset. Nitrogen fertilization decreased soil pH, and increased soil organic carbon (C) and available N contents. Bacterial taxonomic diversity was decreased by N fertilization alone, but was increased by NPK fertilization. The effect of N fertilization on bacterial diversity varied with soil texture and water management, but was independent of crop type or N application rate. Changes in bacterial diversity were positively related to both soil pH and organic C content under N fertilization alone, but only to soil organic C under NPK fertilization. Microbial biomass C decreased with decreasing bacterial diversity under long-term N fertilization. Nitrogen fertilization increased the relative abundance of Proteobacteria and Actinobacteria, but reduced the abundance of Acidobacteria, consistent with the general life history strategy theory for bacteria. The positive correlation between N application rate and the relative abundance of Actinobacteria indicates that increased N availability favored the growth of Actinobacteria. This first global analysis of long-term N and NPK fertilization that differentially affects bacterial diversity and community composition provides a reference for nutrient management strategies for maintaining belowground microbial diversity in agro-ecosystems worldwide.

Shifts in prokaryotic communities under forest and grassland within a tropical mosaic landscape

The Anthropocene is linked to massive land use changes as a result of human activity. While aboveground changes in biodiversity are well documented, the effects on belowground microbial communities are less understood, yet could impact on many ecosystem functions. Here we aimed to identify differences in belowground microbial diversity between forest and grassland sites in a humid tropical mosaic landscape in Papua New Guinea. Using DNA-based amplicon sequencing targeting the 16S rRNA gene, prokaryotic community composition was assessed from surface soil samples. The composition of prokaryotic communities (beta diversity) differed between forest and grassland sites despite maintaining similar richness (alpha diversity) levels. Changes in community structure were small at higher taxonomic levels, but strong at the operational taxonomic unit (OTU) level but for a small subset of taxa. Changes in community composition between sites (based on Bray-Curtis distance) reflected a large rearrangement with species assemblage (OTU) differing by 68%. The results suggest that ecosystem change in this landscape leads to ecological filtering and selection at lower, but not higher taxonomic levels.

Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve.

Invasion by exotic plant species can alter ecosystem function and reduce native plant diversity, but relatively little is known about their effects on belowground microbial communities. Here we investigated the effects of exotic cordgrass (Spartina alterniflora) invasion on the distribution of soil bacterial communities in a mangrove nature reserve of the Jiulong River Estuary, southeast China using high-throughput sequencing of 16S rRNA gene and multivariate statistical analysis. Our results showed that S. alterniflora invasion altered soil properties, and significantly increased soil bacterial taxa richness, primarily by stimulating an increase in conditionally rare or rare taxa, and changes in community composition and function. Abundant, conditionally rare and rare subcommunities exhibited similar response patterns to environment changes, with both conditionally rare and rare taxa showing a stronger response than abundant ones. Habitat generalists were detected among abundant, conditionally rare and rare taxa, whereas habitat specialists were only identified among conditionally rare taxa and rare taxa. In addition, we found that vegetation was the key factor driving these patterns. However, our comparative analysis indicated that both environmental selection, and neutral process, significantly contributed to soil bacterial community assembly. These results could improve the understanding of the microbial processes and mechanisms of cordgrass invasion, and offer empirical data of use in the restoration and management of the mangrove wetlands.

Unravelling the composition of soil belowground microbial community before sowing transgenic cotton

Soils harbour enormously diverse bacterial communities that interact specifically with plants generating beneficial interactions between them. This study was the first approach to assess bacterial communities before sowing with three cotton genotypes, including both transgenic and conventional ones. The structure of bacterial communities was identified using the next generation sequencing analysis, ion torrent PGM (Personal Genome Machine™) sequencer technology, based on the V2–V3 16S rRNA gene region. Quantitative insights into microbial ecology pipeline were used to identify the structure and diversity of bacterial communities in bulk soil samples collected in the northeast of Mexico. Bulk soil textures and chemical properties, including most nutrients, were homogeneous in these bulk soil samples. Relative abundance analysis showed similar bacterial community structures. Dominant taxonomic phyla were Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria, Gemmatimonadetes and Bacteroidetes, whereas the main families were Bacillaceae, Chitinophagaceae and Rhodospirillaceae with an abundance average of BS1 (bulk soil sample), BS2 and BS3 (24.85, 19.74 and 19.71%, respectively). Alpha diversity analysis showed a high diversity (Shannon and Simpson index) and a large value of the observed species found in bulk soils samples. These results allowed establishing the previous bacterial structural community in an unused soil before sowing it with a transgenic crop for the first time.

Decomposition of Leaves and Fine Roots in Three Subtropical Plantations in China Affected by Litter Substrate Quality and Soil Microbial Community

Leaf and root litter decomposition has been a major research focus. However, the possible effects of belowground microbial community structure and diversity on this process are poorly understood. Understanding the biochemical mechanisms controlling aboveground decomposition processes is important to predict the changes of soil carbon and nutrient cycling in response to changes of forest management regimes. Here, we explore the biochemical controls of leaf and fine root decomposition in three subtropical plantations (Ford Erythrophleum (Erythrophleum fordii Oliver), Masson Pine (Pinus massoniana Lamb.)), and a mixed plantation containing both species) using the litterbag method, and soil microbial communities were determined using phospholipid fatty acid profiles. Overall, leaves decomposed more rapidly than fine roots, potentially due to the faster degradation of their cellulose component, but not lignin. In addition, leaf and fine root decomposition rates varied among plantations, being higher in E. fordii and lower in P. massoniana. Substrate quality such as N, Ca, lignin concentration, and C/N ratio were responsible for the decomposition rate changes among plantation types. Moreover, we used redundancy analysis to examine the relationships between litter decomposition and soil microbial community composition and diversity. Results revealed that actinobacteria and arbuscular mycorrhizal fungi community were the key determinants affecting leaf and fine root litter decomposition, respectively. Our work demonstrates that litter decomposition was linked to substrate quality and to the structure of soil microbial communities, and evidences the probable role of E. fordii in increasing soil nutrient availability, especially N, P and Ca. Additional data on phospholipid fatty acid (PLFA) or DNA marker groups within the litterbags over time may provide insights into litter decomposition dynamics, which represents potential objectives for future long-term decomposition studies.

Response of soil microbial community composition and function to a bottomland forest restoration intensity gradient

Terrestrial ecosystems are globally under threat of loss or degradation. To compensate for the impacts incurred by loss and/or degradation, efforts to restore ecosystems are being undertaken. These efforts often focus on restoring the aboveground plant community with the expectation that the belowground microbial community will follow suit. This ‘Field of Dreams’ expectation – if you build it, they will come – makes untested assumptions about how microbial communities and their functions will respond to aboveground-focused restoration. To determine if restoration of aboveground plant communities equates to restoration of belowground microbial communities, we assessed the effects of four forest restoration treatments – varying in intensity from unmanaged to interplanting tree species – on microbial (i.e. prokaryotic and fungal) community composition and function (i.e. catabolic profiles and extracellular enzyme activities). Additionally, effects of the restoration treatments were compared to both degraded (i.e. active arable cultivation) and target endpoint communities (i.e. remnant bottomland forest) to determine the trajectory of intensifying aboveground restoration efforts on microbial communities. Approximately 16 years after the initiation of the restoration treatments, prokaryotic and fungal community composition, and microbial function in the four restoration treatments were intermediate to the endpoint communities. Surprisingly, intensification of aboveground restoration efforts led to few differences among the four restoration treatments and increasing intensification did not consistently lead to microbial communities with greater similarity in composition and function to the target remnant forest communities. Together these results suggest that belowground microbial community composition and function will respond little to, or will lag markedly behind, intensifying aboveground restoration efforts. Reliance on a ‘Field of Dreams’ approach, even if you build it better, may still lead to belowground microbial communities that remain uncoupled from aboveground communities. Importantly, our findings suggest that restoring aboveground vegetation may not lead to the intended restoration of belowground microbial communities and the ecosystem processes they mediate.

Biodiversity effects on ecosystem functioning in a 15-year grassland experiment: Patterns, mechanisms, and open questions

Biodiversity effects on ecosystem functioning in a 15-year grassland experiment: Patterns, mechanisms, and open questions

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity.

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se.

Leaf endophytic fungus interacts with precipitation to alter belowground microbial communities in primary successional dunes.

Understanding interactions between above- and belowground components of ecosystems is an important next step in community ecology. These interactions may be fundamental to predicting ecological responses to global change because indirect effects occurring through altered species interactions can outweigh or interact with the direct effects of environmental drivers. In a multiyear field experiment (2010-2015), we tested how experimental addition of a mutualistic leaf endophyte (Epichloë amarillans) associated with American beachgrass (Ammophila breviligulata) interacted with an altered precipitation regime (±30%) to affect the belowground microbial community. Epichloë addition increased host root biomass at the plot scale, but reduced the length of extraradical arbuscular mycorrhizal (AM) fungal hyphae in the soil. Under ambient precipitation alone, the addition of Epichloë increased root biomass per aboveground tiller and reduced the diversity of AM fungi in A. breviligulata roots. Furthermore, with Epichloë added, the diversity of root-associated bacteria declined with higher soil moisture, whereas in its absence, bacterial diversity increased with higher soil moisture. Thus, the aboveground fungal mutualist not only altered the abundance and composition of belowground microbial communities but also affected how belowground communities responded to climate, suggesting that aboveground microbes have potential for cascading influences on community dynamics and ecosystem processes that occur belowground.

Interactive effects of multiple climate change factors on ammonia oxidizers and denitrifiers in a temperate steppe.

Global climate change could have profound effects on belowground microbial communities and subsequently affect soil biogeochemical processes. The interactive effects of multiple co-occurring climate change factors on microbially mediated processes are not well understood. A four-factorial field experiment with elevated CO2, watering, nitrogen (N) addition and night warming was conducted in a temperate steppe of northern China. Real-time polymerase chain reaction and terminal-restriction fragment length polymorphism, combined with clone library techniques, were applied to examine the effects of those climate change factors on N-related microbial abundance and community composition. Only the abundance of ammonia-oxidizing bacteria significantly increased by nitrogen addition and decreased by watering. The interactions of watering × warming on the bacterial amoA community and warming × nitrogen addition on the nosZ community were found. Redundancy analysis indicated that the ammonia-oxidizing archaeal community was affected by total N and total carbon, while the community of bacterial amoA and nosZ were significantly affected by soil pH. According to a structural equation modeling analysis, climate change influenced net primary production indirectly by altering microbial abundance and activities. These results indicated that microbial responses to the combination of chronic global change tend to be smaller than expected from single-factor global change manipulations.

Does the presence of large down wood at the time of a forest fire impact soil recovery?

Fire may remove or create dead wood aboveground, but it is less clear how high severity burning of soils affects belowground microbial communities and soil processes, and for how long. In this study, we investigated soil fungal and bacterial communities and biogeochemical responses of severely burned “red” soil and less severely burned “black” soil from a burned forest on the eastern slope of the Cascade Range in Oregon. Specifically, we examined the effects of burn severity on soil nutrients and microbial communities for 1–4years after wildfire. Soil nutrients were significantly reduced in red soils. Soil fungi and bacteria, assessed with molecular methods, steadily colonized both burn severities and soil biodiversity increased throughout the study showing that microbial communities seem to have the capacity to quickly adjust to extreme disturbances. Although richness did not vary by soil type, the fungal and bacterial community compositions varied with burn severity. This difference was greatest in the early time points following the fire and decreased with time. However, nutrient-limited conditions of red soils were detected for four years after the wildfire and raise concern about soil productivity at these sites.

Ammonia-oxidizing bacteria rather than archaea respond to short-term urea amendment in an alpine grassland

Chemical fertilizers, especially nitrogen (N) and phosphorus (P), are used in grasslands to maximize plant biomass production for livestock. Despite a substantial body of work on how fertilization affects aboveground plant and belowground microbial communities, the short-term response of soil ammonia-oxidizing microbial communities, which play the central role in nitrification, to fertilization is not well understood. The responses of ammonia-oxidizing microbial communities to short-term (3 years) N and/or P additions were investigated in an alpine grassland of the Qinghai-Tibetan Plateau. Quantitative polymerase chain reaction (qPCR) analysis of the amoA genes showed that ammonia-oxidizing archaea (AOA) dominated over ammonia-oxidizing bacteria (AOB) in non-amended soil. Short-term urea addition significantly increased the abundance of AOB, whereas AOA abundance remained unchanged, resulting in a shift from AOA to AOB dominance, which suggests that AOB are likely to be more important in the first step of the nitrification following urea amendment. Pyrosequencing demonstrated a significant shift in AOB but not AOA community composition within short-term N fertilizer plots, indicating that AOB community composition was more sensitive than AOA in response to urea amendment. This study demonstrated that the abundance and composition of AOA and AOB communities responded differently to 3 years of urea addition, suggesting that N fertilizer may be an important controller of ammonia-oxidizing microbial communities in managed alpine grasslands, such as those of the Qinghai-Tibet Plateau.

Differential responses of soil bacterial communities to long-term N and P inputs in a semi-arid steppe

Both nitrogen (N) and phosphorus (P) may limit plant production in steppes and affect plant community structure. However, few studies have explored in detail the differences and similarities in the responses of belowground microbial communities to long-term N and P inputs. Using a high-throughput Illumina Miseq sequencing platform, we characterized the bacterial communities in a semi-arid steppe subjected to long-term N or P additions. Our results showed that both the Chao richness and Shannon's diversity were negatively correlated to N input rate, while only Chao richness was significantly and negatively correlated to P input rate. Also, both N and P additions altered the bacterial community structure. The bacterial community between plots of the same N or P input rate was much more dissimilar with the higher input level, indicating more severe niche differentiation in pots with higher N or P input. N Inputs significantly increased the relative abundance of the predicted copiotrophic groups (Proteobacteria and Firmicutes) but reduced the predicted oligotrophic groups (Acidobacteria, Nitrospirae, Chloroflexi), with the order Rhizobiales being most affected. P additions significantly affected only two phyla (Armatimonadetes and Chlorobi), which were positively correlated with P source. Results from the structural equation modelling (SEM) showed that N additions affected the bacterial community primarily by changing the pH, while P additions did so mainly by improving P availability. Our results suggest that the below-ground bacterial communities are more sensitive to N inputs, but P inputs can also play an important role in bacterial niche differentiation. These findings improve our understanding of bacterial responses to N and P inputs, and their impacts on bacterial-mediated processes, especially in the context of increasing anthropogenic nutrient inputs.

Metagenomic reconstruction of nitrogen cycling pathways in a CO2-enriched grassland ecosystem

The nitrogen (N) cycle is a collection of important biogeochemical pathways mediated by microbial communities and is an important constraint in response to elevated CO2 in many terrestrial ecosystems. Previous studies attempting to relate soil N cycling to microbial genetic data mainly focused on a few gene families by PCR, protein assays and functional gene arrays, leaving the taxonomic and functional composition of soil microorganisms involved in the whole N cycle less understood. In this study, 24 soil samples were collected from the long-term experimental site, BioCON, in 2009. A shotgun metagenome sequencing approach was employed to survey the microbial gene families involved in soil N cycle in the grassland that had been exposed to elevated CO2 (eCO2) for >12 years. In addition to evaluating the responses of major N cycling gene families to long-term eCO2, we also aimed to characterize the taxonomic and functional composition of these gene families involved in soil N transformations. At the taxonomic level, organic N metabolism and nitrate reduction had the most diverse microbial species involved. The distinct taxonomic composition of different N cycling processes suggested that the complex N cycle in natural ecosystems was a result of multiple processes by many different microorganisms. Belowground microbial communities that mediate N cycling responded to eCO2 in several different ways, including through stimulated abundances of the gene families related with organic decomposition, dissimilatory nitrate reduction, and N2 fixation, and suppressed abundances of the gene families in glutamine synthesis and anammox. This study provides a genetic basis of the microorganisms involved in key processes in the N cycle in complex ecosystems, and shows that long-term eCO2 selectively affects N cycling pathways instead of tuning up every process.