Elevated CO₂ influences microbial carbon and nitrogen cycling

New Aspects of the Effects of Climate Change on Interactions Between Plants and Microbiomes: A Review

One of the most talked about issues of the 21st century is climate change, as it affects not just our health but also forestry, agriculture, biodiversity, the ecosystem, and the energy supply. Greenhouse gases are the primary cause of climate change, having dramatic effects on the environment. Climate change has an impact on the function and composition of the terrestrial microbial community both directly and indirectly. Changes in the prevailing climatic conditions brought about by climate change will lead to modifications in plant physiology, root exudation, signal alteration, and the quantity, makeup, and diversity of soil microbial communities. Microbiological activity is very crucial in organic production systems due to the organic origin of microorganisms. Microbes that benefit crop plants are known as plant growth-promoting microorganisms. Thus, the effects of climate change on the environment also have an impact on the abilities of beneficial bacteria to support plant growth, health, and root colonization. In this review, we have covered the effects of temperature, precipitation, drought, and CO2 on plant-microbe interactions, as well as some physiological implications of these changes. Additionally, this paper highlights the ways in which bacteria in plants' rhizosphere react to the dominant climatic conditions in the soil environment. The goal of this study is to analyze the effects of climate change on plant-microbe interactions.

Stimulation of primed carbon under climate change corresponds with phosphorus mineralization in the rhizosphere of soybean

Elevated CO2 and temperature likely alter photosynthetic carbon inputs to soils, which may stimulate soil microbial activity to accelerate the decomposition of soil organic carbon (SOC), liberating more phosphorus (P) into the soil solution. However, this hypothesis on the association of SOC decomposition and P transformation in the plant rhizosphere requires robust soil biochemical evidence, which is critical to nutrient management for the mitigation of soil quality against climate change. This study investigated the microbial functional genes relevant to P mineralization together with priming processes of SOC in the rhizosphere of soybean grown under climate change. Soybean plants were grown under elevated CO2 (eCO2, 700 ppm) combined with warming (+ 2 °C above ambient temperature) in open-top chambers. Photosynthetic carbon flow in the plant-soil continuum was traced with 13CO2 labeling. The eCO2 plus warming treatment increased the primed carbon (C) by 43 % but decreased the NaHCO3-extratable organic P by 33 %. Furthermore, NaHCO3-Po was negatively correlated with phosphatase activity and microbial biomass C. Elevated CO2 increased the abundances of C degradation genes, such as abfA and ManB, and P mineralization genes, such as gcd, phoC and phnK. The results suggested that increased photosynthetic carbon inputs to the rhizosphere of plants under eCO2 plus warming stimulated the microbial population and metabolic functions of both SOC and organic P mineralization. There is a positive relationship between the rhizosphere priming effect and P mineralization. The response of microorganisms to plant-C flow is decisive for coupled C and P cycles, which are likely accelerated under climate change.

The regulation of carbon dioxide on food microorganisms: A review

This review presents a survey of two extremely important technologies about CO2 with the effectiveness of controlling microorganisms - atmospheric pressure CO2-based modified atmosphere packaging (MAP) and high pressure CO2 non-thermal pasteurization (HPCD). CO2-based MAP is effectively in delaying the lag and logarithmic phases of microorganisms by replacing the surrounding air, while HPCD achieved sterilization by subjecting food to either subcritical or supercritical CO2 for some time in a continuous, batch or semi-batch way. In addition to the advantages of healthy, eco-friendly, quality-preserving, effective characteristic, some challenges such as the high drip loss and packaging collapse associated with higher concentration of CO2, the fuzzy mechanisms of oxidative stress, the unproven specific metabolic pathways and biomarkers, etc., in CO2-based MAP, and the unavoidable extraction of bioactive compounds, the challenging application in solid foods with higher efficiency, the difficult balance between optimal sterilization and optimal food quality, etc., in HPCD still need more efforts to overcome. The action mechanism of CO2 on microorganisms, researches in recent years, problems and future perspectives are summarized. When dissolved in solution medium or cellular fluids, CO2 can form carbonic acid (H2CO3), and H2CO3 can further dissociate into bicarbonate ions (HCO3-), carbonate (CO32-) and hydrogen cations (H+) ionic species following series equilibria. The action mode of CO2 on microorganisms may be relevant to changes in intracellular pH, alteration of proteins, enzyme structure and function, alteration of cell membrane function and fluidity, and so on. Nevertheless, the effects of CO2 on microbial biofilms, energy metabolism, protein and gene expression also need to be explored more extensively and deeply to further understand the action mechanism of CO2 on microorganisms.

Elevated atmospheric CO2 concentrations caused a shift of the metabolically active microbiome in vineyard soil

BACKGROUND

Elevated carbon dioxide concentrations (eCO2), one of the main causes of climate change, have several consequences for both vine and cover crops in vineyards and potentially also for the soil microbiome. Hence soil samples were taken from a vineyard free-air CO2 enrichment (VineyardFACE) study in Geisenheim and examined for possible changes in the soil active bacterial composition (cDNA of 16S rRNA) using a metabarcoding approach. Soil samples were taken from the areas between the rows of vines with and without cover cropping from plots exposed to either eCO2 or ambient CO2 (aCO2).

RESULTS

Diversity indices and redundancy analysis (RDA) demonstrated that eCO2 changed the active soil bacterial diversity in grapevine soil with cover crops (p-value 0.007). In contrast, the bacterial composition in bare soil was unaffected. In addition, the microbial soil respiration (p-values 0.04-0.003) and the ammonium concentration (p-value 0.003) were significantly different in the samples where cover crops were present and exposed to eCO2. Moreover, under eCO2 conditions, qPCR results showed a significant decrease in 16S rRNA copy numbers and transcripts for enzymes involved in N2 fixation and NO2- reduction were observed using qPCR. Co-occurrence analysis revealed a shift in the number, strength, and patterns of microbial interactions under eCO2 conditions, mainly represented by a reduction in the number of interacting ASVs and the number of interactions.

CONCLUSIONS

The results of this study demonstrate that eCO2 concentrations changed the active soil bacterial composition, which could have future influence on both soil properties and wine quality.

Soil metatranscriptome demonstrates a shift in C, N, and S metabolisms of a grassland ecosystem in response to elevated atmospheric CO2

Soil organisms play an important role in the equilibrium and cycling of nutrients. Because elevated CO2 (eCO2) affects plant metabolism, including rhizodeposition, it directly impacts the soil microbiome and microbial processes. Therefore, eCO2 directly influences the cycling of different elements in terrestrial ecosystems. Hence, possible changes in the cycles of carbon (C), nitrogen (N), and sulfur (S) were analyzed, alongside the assessment of changes in the composition and structure of the soil microbiome through a functional metatranscriptomics approach (cDNA from mRNA) from soil samples taken at the Giessen free-air CO2 enrichment (Gi-FACE) experiment. Results showed changes in the expression of C cycle genes under eCO2 with an increase in the transcript abundance for carbohydrate and amino acid uptake, and degradation, alongside an increase in the transcript abundance for cellulose, chitin, and lignin degradation and prokaryotic carbon fixation. In addition, N cycle changes included a decrease in the transcript abundance of N2O reductase, involved in the last step of the denitrification process, which explains the increase of N2O emissions in the Gi-FACE. Also, a shift in nitrate (NO 3 - ) metabolism occurred, with an increase in transcript abundance for the dissimilatoryNO 3 - reduction to ammonium (NH 4 + ) (DNRA) pathway. S metabolism showed increased transcripts for sulfate (SO 4 2 - ) assimilation under eCO2 conditions. Furthermore, soil bacteriome, mycobiome, and virome significantly differed between ambient and elevated CO2 conditions. The results exhibited the effects of eCO2 on the transcript abundance of C, N, and S cycles, and the soil microbiome. This finding showed a direct connection between eCO2 and the increased greenhouse gas emission, as well as the importance of soil nutrient availability to maintain the balance of soil ecosystems.

Cysteine reduced the inhibition of CO2 on heterotrophic denitrification: Restoring redox balance, facilitating iron acquisition and carbon metabolism

The direct effect of CO₂ on denitrification has attracted great attention currently. Our previous studies have confirmed that CO₂ inhibited heterotrophic denitrification and caused high nitrite accumulation and nitrous oxide emission. Cysteine is a widely reported bio-accelerator; however, its effect on denitrification under CO₂ exposure remains unknown. In this paper, the effect of cysteine on heterotrophic denitrification and its mechanisms under CO₂ exposure were explored with the model denitrifier, Paracoccus denitrificans. We observed that total nitrogen removal increased from 17.9% to 90.4% as cysteine concentration increased from 0 to 50 μM, probably due to restoration of cell growth and viability. Further study showed that cysteine reduced the inhibition of CO₂ on denitrification due to multiple positive influences: (1) regulating glutathione metabolism to eliminate intracellular reactive nitrogen species (RNS), while reducing extracellular polymeric substances (EPS) levels and altering its composition, ultimately restoring cell membrane integrity (2) facilitating the transport and metabolism of carbon sources to increase NADH production, and (3) increasing intracellular iron and up-regulating the expression of key iron transporters genes (AfuA, AfuB, ExbB and TonB) to restore the transport and consumption of electron. This study suggests that cysteine can be added to recover heterotrophic denitrification performance after inhibition by elevated CO₂.

Elevated Atmospheric CO2 Modifies Mostly the Metabolic Active Rhizosphere Soil Microbiome in the Giessen FACE Experiment

Elevated levels of atmospheric CO2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO2 enrichment (Gi-FACE) experiment on a permanent grassland site near Giessen, Germany. The aim was to assess the effects of increased C supply into the soil, due to elevated CO2, on the active soil microbiome composition. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and the obtained data were processed for a compositional data analysis calculating diversity indices and differential abundance analyses. The structure of the metabolic active microbiome in the rhizospheric soil showed a clear separation between elevated and ambient CO2 (p = 0.002); increased atmospheric CO2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO2 had no major influence on the structure of the bulk soil microbiome (p = 0.097). Differential abundance results demonstrated that 42 bacterial genera were stimulated under elevated CO2. The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO2 increase of climate change will significantly shift the microbiome structure in the rhizosphere.

Elevated pCO2 alters the interaction patterns and functional potentials of rearing seawater microbiota

Mean oceanic CO₂ values have already risen and are expected to rise further on a global scale. Elevated pCO₂ (eCO₂) changes the bacterial community in seawater. However, the ecological association of seawater microbiota and related geochemical functions are largely unknown. We provide the first evidence that eCO₂ alters the interaction patterns and functional potentials of microbiota in rearing seawater of the swimming crab, Portunus trituberculatus. Network analysis showed that eCO₂ induced a simpler and more modular bacterial network in rearing seawater, with increased negative associations and distinct keystone taxa. Using the quantitative microbial element cycling method, nitrogen (N) and phosphorus (P) cycling genes exhibited the highest increase after one week of eCO₂ stress and were significantly associated with keystone taxa. However, the functional potential of seawater bacteria was decoupled from their taxonomic composition and strongly coupled with eCO₂ levels. The changed functional potential of seawater bacteria contributed to seawater N and P chemistry, which was highlighted by markedly decreased NH₃, NH₄⁺-N, and PO₄^3--P levels and increased NO₂^--N and NO₃^--N levels. This study suggests that eCO₂ alters the interaction patterns and functional potentials of seawater microbiota, which lead to the changes of seawater chemical parameters. Our findings provide new insights into the mechanisms underlying the effects of eCO₂ on marine animals from the microbial ecological perspective.

Directional Selection of Microbial Community Reduces Propionate Accumulation in Glycerol and Glucose Anaerobic Bioconversion Under Elevated pCO2

Volatile fatty acid accumulation is a sign of digester perturbation. Previous work showed the thermodynamic limitations of hydrogen and CO₂ in syntrophic propionate oxidation under elevated partial pressure of CO₂ (pCO₂). Here we study the effect of directional selection under increasing substrate load as a strategy to restructure the microbial community and induce cross-protection mechanisms to improve glucose and glycerol conversion performance under elevated pCO₂. After an adaptive laboratory evolution (ALE) process, viable cell density increased and predominant microbial groups were modified: an increase in Methanosaeta and syntrophic propionate oxidizing bacteria (SPOB) associated with the Smithella genus was found with glycerol as the substrate. A modest increase in SPOB along with a shift in the predominance of Methanobacterium toward Methanosaeta was observed with glucose as the substrate. The evolved inoculum showed affected diversity within archaeal spp. under 5 bar initial pCO₂; however, higher CH₄ yield resulted from enhanced propionate conversion linked to the community shifts and biomass adaptation during the ALE process. Moreover, the evolved inoculum attained increased cell viability with glucose and a marginal decrease with glycerol as the substrate. Results showed differences in terms of carbon flux distribution using the evolved inoculum under elevated pCO₂: glucose conversion resulted in a higher cell density and viability, whereas glycerol conversion led to higher propionate production whose enabled conversion reflected in increased CH₄ yield. Our results highlight that limited propionate conversion at elevated pCO₂ resulted from decreased cell viability and low abundance of syntrophic partners. This limitation can be mitigated by promoting alternative and more resilient SPOB and building up biomass adaptation to environmental conditions via directional selection of microbial community.

Climate change effects on plant-soil feedbacks and consequences for biodiversity and functioning of terrestrial ecosystems

Plant-soil feedbacks (PSFs) are interactions among plants, soil organisms, and abiotic soil conditions that influence plant performance, plant species diversity, and community structure, ultimately driving ecosystem processes. We review how climate change will alter PSFs and their potential consequences for ecosystem functioning. Climate change influences PSFs through the performance of interacting species and altered community composition resulting from changes in species distributions. Climate change thus affects plant inputs into the soil subsystem via litter and rhizodeposits and alters the composition of the living plant roots with which mutualistic symbionts, decomposers, and their natural enemies interact. Many of these plant-soil interactions are species-specific and are greatly affected by temperature, moisture, and other climate-related factors. We make a number of predictions concerning climate change effects on PSFs and consequences for vegetation-soil-climate feedbacks while acknowledging that they may be context-dependent, spatially heterogeneous, and temporally variable.

Potential CO2 intrusion in near-surface environments: a review of current research approaches to geochemical processes

Carbon dioxide (CO₂) capture and storage (CCS) plays a crucial role in reducing carbon emissions to the atmosphere. However, gas leakage from deep storage reservoirs, which may flow back into near-surface and eventually to the atmosphere, is a major concern associated with this technology. Despite an increase in research focusing on potential CO₂ leakage into deep surface features and aquifers, a significant knowledge gap remains in the geochemical changes associated with near-surface. This study reviews the geochemical processes related to the intrusion of CO₂ into near-surface environments with an emphasis on metal mobilization and discusses about the geochemical research approaches, recent findings, and current knowledge gaps. It is found that the intrusion of CO₂(g) into near-surface likely induces changes in pH, dissolution of minerals, and potential degradation of surrounding environments. The development of adequate geochemical research approaches for assessing CO₂ leakage in near-surface environments, using field studies, laboratory experiments, and/or geochemical modeling combined with isotopic tracers, has promoted extensive surveys of CO₂-induced reactions. However, addressing knowledge gaps in geochemical changes in near-surface environments is fundamental to advance current knowledge on how CO₂ leaks from storage sites and the consequences of this process on soil and water chemistry. For reliable detection and risk management of the potential impact of CO₂ leakage from storage sites on the environmental chemistry, currently available geochemical research approaches should be either combined or used independently (albeit in a manner complementarily to one another), and the results should be jointly interpreted.

Effects of elevated carbon dioxide on environmental microbes and its mechanisms: A review

Before the industrial revolution, the atmospheric CO₂ concentration was 180-330 ppm; however, fossil-fuel combustion and forest destruction have led to increased atmospheric CO₂ concentration. CO₂ capture and storage is regarded as a promising strategy to prevent global warming and ocean acidification and to alleviate elevated atmospheric CO₂ concentration, but the leakage of CO₂ from storage system can lead to rapid acidification of the surrounding circumstance, which might cause negative influence on environmental microbes. The effects of elevated CO₂ on microbes have been reported extensively, but the review regarding CO₂ affecting different environmental microorganisms has never been done previously. Also, the mechanisms of CO₂ affecting environmental microorganisms are usually contributed to the change of pH values, while the direct influences of CO₂ on microorganisms were often neglected. This paper aimed to provide a systematic review of elevated CO₂ affecting environmental microbes and its mechanisms. Firstly, the influences of elevated CO₂ and potential leakage of CO₂ from storage sites on community structures and diversity of different surrounding environmental microbes were assessed and compared. Secondly, the adverse impacts of CO₂ on microbial growth, cell morphology and membranes, bacterial spores, and microbial metabolism were introduced. Then, based on biochemical principles and knowledge of microbiology and molecular biology, the fundamental mechanisms of the influences of carbon dioxide on environmental microbes were discussed from the aspects of enzyme activity, electron generation and transfer, and key gene and protein expressions. Finally, key questions relevant to the environmental effect of CO₂ that need to be answered in the future were addressed.

Bacterial community response to a preindustrial-to-future CO2 gradient is limited and soil specific in Texas Prairie grassland

Rising atmospheric CO₂ concentration directly stimulates plant productivity and affects nutrient dynamics in the soil. However, the influence of CO₂ enrichment on soil bacterial communities remains elusive, likely due to their complex interactions with a wide range of plant and soil properties. Here, we investigated the bacterial community response to a decade long preindustrial-to-future CO₂ gradient (250-500 ppm) among three contrasting soil types using 16S rRNA gene amplicon sequencing. In addition, we examined the effect of seasonal variation and plant species composition on bacterial communities. We found that Shannon index (H') and Faith's phylogenetic diversity (PD) did not change in response to the CO₂ gradient (R²  = 0.01, p > 0.05). CO₂ gradient and season also had a negligible effect on overall community structure, although silty clay soil communities were better structured on a CO₂ gradient (p < 0.001) among three soils. Similarly, CO₂ gradient had no significant effect on the relative abundance of different phyla. However, we observed soil-specific variation of CO₂ effects in a few individual families. For example, the abundance of Pirellulaceae family decreased linearly with CO₂ gradient, but only in sandy loam soils. Conversely, the abundance of Micromonosporaceae and Gaillaceae families increased with CO₂ gradient in clay soils. Soil water content (SWC) and nutrient properties were the key environmental constraints shaping bacterial community structure, one manifestation of which was a decline in bacterial diversity with increasing SWC. Furthermore, the impact of plant species composition on community structure was secondary to the strong influence of soil properties. Taken together, our findings indicate that bacterial communities may be largely unresponsive to indirect effects of CO₂ enrichment through plants. Instead, bacterial communities are strongly regulated by edaphic conditions, presumably because soil differences create distinct environmental niches for bacteria.

Divergent Responses of the Diazotrophic Microbiome to Elevated CO2 in Two Rice Cultivars

The species-specific responses of plant growth to elevated atmospheric CO2 concentration (eCO2) could lead to N limitation and potentially influence the sustainability of ecosystem. Questions remain unanswered with regards to the response of soil N2-fixing community to eCO2 when developing high-yielding agroecosystem to dampen the future rate of increase in CO2 levels and associated climate warming. This study demonstrates the divergent eCO2 influences on the paddy diazotrophic community between weak- and strong-responsive rice cultivars. In response to eCO2, the diazotrophic abundance increased more for the strong-responsive cultivar treatments than for the weak-responsive ones. Only the strong-responsive cultivars decreased the alpha diversity and separated the composition of diazotrophic communities in response to eCO2. The topological indices of the ecological networks further highlighted the different co-occurrence patterns of the diazotrophic microbiome in rice cultivars under eCO2. Strong-responsive cultivars destabilized the diazotrophic community by complicating and centralizing the co-occurrence network as well as by shifting the hub species from Bradyrhizobium to Dechloromonas in response to eCO2. On the contrary, the network pattern of the weak-responsive cultivars was simplified and decentralized in response to eCO2, with the hub species shifting from Halorhodospira under aCO2 to Sideroxydans under eCO2. Collectively, the above information indicates that the strong-responsive cultivars could potentially undermine the belowground ecosystem from the diazotrophs perspective in response to eCO2. This information highlights that more attention should be paid to the stability of the belowground ecosystem when developing agricultural strategies to adapt prospective climatic scenarios by growing high-yielding crop cultivars under eCO2.

Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers

Numerous studies have shown that the continuous increase of atmosphere CO2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO2 (eCO2) at different soil depth profiles in forest ecosystems. Here, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO2 significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO2 at both soil depths, although the stimulation effect of eCO2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO3-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO2 increases.IMPORTANCE The concentration of atmospheric carbon dioxide (CO2) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO2 (eCO2) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO2 at both soil depths. More functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO2 at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.

Soil Conditions Rather Than Long-Term Exposure to Elevated CO2 Affect Soil Microbial Communities Associated with N-Cycling

Continuously rising atmospheric CO₂ concentrations may lead to an increased transfer of organic C from plants to the soil through rhizodeposition and may affect the interaction between the C- and N-cycle. For instance, fumigation of soils with elevated CO₂ (eCO₂) concentrations (20% higher compared to current atmospheric concentrations) at the Giessen Free-Air Carbon Dioxide Enrichment (GiFACE) sites resulted in a more than 2-fold increase of long-term N₂O emissions and an increase in dissimilatory reduction of nitrate compared to ambient CO₂ (aCO₂). We hypothesized that the observed differences in soil functioning were based on differences in the abundance and composition of microbial communities in general and especially of those which are responsible for N-transformations in soil. We also expected eCO₂ effects on soil parameters, such as on nitrate as previously reported. To explore the impact of long-term eCO₂ on soil microbial communities, we applied a molecular approach (qPCR, T-RFLP, and 454 pyrosequencing). Microbial groups were analyzed in soil of three sets of two FACE plots (three replicate samples from each plot), which were fumigated with eCO₂ and aCO₂, respectively. N-fixers, denitrifiers, archaeal and bacterial ammonia oxidizers, and dissimilatory nitrate reducers producing ammonia were targeted by analysis of functional marker genes, and the overall archaeal community by 16S rRNA genes. Remarkably, soil parameters as well as the abundance and composition of microbial communities in the top soil under eCO₂ differed only slightly from soil under aCO₂. Wherever differences in microbial community abundance and composition were detected, they were not linked to CO₂ level but rather determined by differences in soil parameters (e.g., soil moisture content) due to the localization of the GiFACE sets in the experimental field. We concluded that +20% eCO₂ had little to no effect on the overall microbial community involved in N-cycling in the soil but that spatial heterogeneity over extended periods had shaped microbial communities at particular sites in the field. Hence, microbial community composition and abundance alone cannot explain the functional differences leading to higher N₂O emissions under eCO₂ and future studies should aim at exploring the active members of the soil microbial community.

The Diversity and Co-occurrence Patterns of N₂-Fixing Communities in a CO₂-Enriched Grassland Ecosystem

Diazotrophs are the major organismal group responsible for atmospheric nitrogen (N2) fixation in natural ecosystems. The extensive diversity and structure of N2-fixing communities in grassland ecosystems and their responses to increasing atmospheric CO2 remain to be further explored. Through pyrosequencing of nifH gene amplicons and extraction of nifH genes from shotgun metagenomes, coupled with co-occurrence ecological network analysis approaches, we comprehensively analyzed the diazotrophic community in a grassland ecosystem exposed to elevated CO2 (eCO2) for 12 years. Long-term eCO2 increased the abundance of nifH genes but did not change the overall nifH diversity and diazotrophic community structure. Taxonomic and phylogenetic analysis of amplified nifH sequences suggested a high diversity of nifH genes in the soil ecosystem, the majority belonging to nifH clusters I and II. Co-occurrence ecological network analysis identified different co-occurrence patterns for different groups of diazotrophs, such as Azospirillum/Actinobacteria, Mesorhizobium/Conexibacter, and Bradyrhizobium/Acidobacteria. This indicated a potential attraction of non-N2-fixers by diazotrophs in the soil ecosystem. Interestingly, more complex co-occurrence patterns were found for free-living diazotrophs than commonly known symbiotic diazotrophs, which is consistent with the physical isolation nature of symbiotic diazotrophs from the environment by root nodules. The study provides novel insights into our understanding of the microbial ecology of soil diazotrophs in natural ecosystems.

The impact of elevated carbon dioxide on the phosphorus nutrition of plants: a review

BACKGROUND

Increasing attention is being focused on the influence of rapid increases in atmospheric CO2 concentration on nutrient cycling in ecosystems. An understanding of how elevated CO2 affects plant utilization and acquisition of phosphorus (P) will be critical for P management to maintain ecosystem sustainability in P-deficient regions.

SCOPE

This review focuses on the impact of elevated CO2 on plant P demand, utilization in plants and P acquisition from soil. Several knowledge gaps on elevated CO2-P associations are highlighted.

CONCLUSIONS

Significant increases in P demand by plants are likely to happen under elevated CO2 due to the stimulation of photosynthesis, and subsequent growth responses. Elevated CO2 alters P acquisition through changes in root morphology and increases in rooting depth. Moreover, the quantity and composition of root exudates are likely to change under elevated CO2, due to the changes in carbon fluxes along the glycolytic pathway and the tricarboxylic acid cycle. As a consequence, these root exudates may lead to P mobilization by the chelation of P from sparingly soluble P complexes, by the alteration of the biochemical environment and by changes to microbial activity in the rhizosphere. Future research on chemical, molecular, microbiological and physiological aspects is needed to improve understanding of how elevated CO2 might affect the use and acquisition of P by plants.

Responses of Aromatic-Degrading Microbial Communities to Elevated Nitrate in Sediments

A high number of aromatic compounds that have been released into aquatic ecosystems have accumulated in sediment because of their low solubility and high hydrophobicity, causing significant hazards to the environment and human health. Since nitrate is an essential nitrogen component and a more thermodynamically favorable electron acceptor for anaerobic respiration, nitrate-based bioremediation has been applied to aromatic-contaminated sediments. However, few studies have focused on the response of aromatic-degrading microbial communities to nitrate addition in anaerobic sediments. Here we hypothesized that high nitrate inputs would stimulate aromatic-degrading microbial communities and their associated degrading processes, thus increasing the bioremediation efficiency in aromatic compound-contaminated sediments. We analyzed the changes of key aromatic-degrading genes in the sediment samples from a field-scale site for in situ bioremediation of an aromatic-contaminated creek in the Pearl River Delta before and after nitrate injection using a functional gene array. Our results showed that the genes involved in the degradation of several kinds of aromatic compounds were significantly enriched after nitrate injection, especially those encoding enzymes for central catabolic pathways of aromatic compound degradation, and most of the enriched genes were derived from nitrate-reducing microorganisms, possibly accelerating bioremediation of aromatic-contaminated sediments. The sediment nitrate concentration was found to be the predominant factor shaping the aromatic-degrading microbial communities. This study provides new insights into our understanding of the influences of nitrate addition on aromatic-degrading microbial communities in sediments.

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest

Background

Tropical rainforests cover over 50 % of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology.

Results

Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure.

Conclusions

Overall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0491-8) contains supplementary material, which is available to authorized users.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0-5 cm and 5-15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems.

Ecological understanding of root-infecting fungi using trait-based approaches

Classification schemes have been popular to tame the diversity of root-infecting fungi. However, the usefulness of these schemes is limited to descriptive purposes. We propose that a shift to a multidimensional trait-based approach to disentangle the saprotrophic-symbiotic continuum will provide a better framework to understand fungal evolutionary ecology. Trait information reflecting the separation of root-infecting fungi from free-living soil relatives will help to understand the evolutionary process of symbiosis, the role that species interactions play in maintaining their large diversity in soil and in planta, and their contributions at the ecosystem level. Methodological advances in several areas such as microscopy, plant immunology, and metatranscriptomics represent emerging opportunities to populate trait databases.

Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments

Nitrate is an important nutrient and electron acceptor for microorganisms, having a key role in nitrogen (N) cycling and electron transfer in anoxic sediments. High-nitrate inputs into sediments could have a significant effect on N cycling and its associated microbial processes. However, few studies have been focused on the effect of nitrate addition on the functional diversity, composition, structure and dynamics of sediment microbial communities in contaminated aquatic ecosystems with persistent organic pollutants (POPs). Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants including polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons (PAHs), before and after nitrate injection using a comprehensive functional gene array (GeoChip 4.0). Our results showed that the sediment microbial community functional composition and structure were markedly altered, and that functional genes involved in N-, carbon (C)-, sulfur (S)-and phosphorus (P)- cycling processes were highly enriched after nitrate injection, especially those microorganisms with diverse metabolic capabilities, leading to potential in situ bioremediation of the contaminated sediment, such as PBDE and PAH reduction/degradation. This study provides new insights into our understanding of sediment microbial community responses to nitrate addition, suggesting that indigenous microorganisms could be successfully stimulated for in situ bioremediation of POPs in contaminated sediments with nitrate addition.