Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil

Plant root carbon inputs drive methane production in tropical peatlands

Tropical peatlands are carbon-dense ecosystems that are significant sources of atmospheric methane (CH4). Recent work has demonstrated the importance of trees as an emission pathway for CH4 from the peat to the atmosphere. However, there remain questions over the processes of CH4 production in these systems and how they relate to substrate supply. Principally, these questions relate to the relative contribution of recent photosynthetically fixed carbon, released as root exudates, versus carbon substrate supply from the slowly decomposing peat matrix to CH4 emissions within these ecosystems. Here, we examined the role of root inputs in regulating CH4 production inferred from soil emissions using a combination of in situ tree girdling, in situ13C natural abundance labelling via stem injections, and a 13CO2 labelling of transplanted plants of two contrasting plant functional types, a broadleaved evergreen tree, and a canopy palm. Girdling of broadleaved evergreen trees reduced CH4 fluxes by up to 67%. Stem injections of trees and palms with a natural abundance label resulted in significant isotopic enrichment of CH4 fluxes, reinforcing the link between root carbon inputs and peat CH4 fluxes. Ex situ13CO2 labelling of plants resulted in significant 13C enrichment of peat CH4 fluxes. Taken together, our results demonstrate for the first time that plant root exudates make a substantial contribution to CH4 production in tropical peatlands.

Advances in studies on the plant rhizosphere microorganisms in wetlands: A visualization analysis based on CiteSpace

Rhizosphere microorganisms and their interactions with plants in wetlands have recently attracted much attention due to their importance in enhancing plant environmental adaptation, removing wetland pollutants, and alleviating climate change. However, the fluctuating hydrological environment of wetlands leads to more complex dynamics in the rhizosphere environment. Research progress and hotspots concerning plant-rhizosphere microorganisms under special wetland environments are still kept unclear. To better understand the current research status, hotspots and trends of rhizosphere microorganisms in wetlands, we used CiteSpace bibliometric software to visualize and analyze 231 English-language publications from the Web of Science core collection database. Here, we reviewed the role played by various countries, institutions, and scholars in the studies of plant rhizosphere microorganisms in wetlands based on cooperation network analysis. We discussed the shift from bioremediation and nutrient removal to rhizosphere microbial community composition as a research hotspot for plant rhizosphere microorganisms in wetlands according to keyword co-occurrence and clustering analysis. Finally, we highlighted that more attention should be paid to the ecological functions of rhizosphere microorganisms in different wetland ecosystems, and the plant‒microbe microinterface processes and interaction patterns should be explored in depth to provide new indicators for the evaluation of wetland ecosystem functions.

Microbial community composition and glyphosate degraders of two soils under the influence of temperature, total organic carbon and pH

Glyphosate can be degraded by soil microorganisms rapidly and is impacted by temperature and soil properties. Enhanced temperature and total organic carbon (TOC) as well as reduced pH increased the rate of 13C315N-glyphosate conversion to CO2 and biogenic non-extractable residues (bioNERs) in a Haplic Chernozem (Muskus et al., 2019) and in a Humic Cambisol (Muskus et al., 2020). To date; however, the combined effect of temperature and TOC or pH on microbial community composition and glyphosate degraders in these two soils has not been investigated. Phospholipid fatty acid [PLFA] biomarker analysis combined with 13C labeling was employed to investigate the effect of two soil properties (pH, TOC) and of three temperatures (10 °C, 20 °C, 30 °C) on soil microorganisms. Before incubation, the properties of a Haplic Chernozem and a Humic Cambisol were adjusted to obtain five treatments: (a) Control (Haplic Chernozem: 2.1% TOC and pH 6.6; Humic Cambisol: 3% TOC and pH 7.0), (b) 3% TOC (Haplic Chernozem) or 4% TOC (Humic Cambisol), (c) 4% TOC (Haplic Chernozem) or 5% TOC (Humic Cambisol), (d) pH 6.0 (Haplic Chernozem) or pH 6.5 (Humic Cambisol), and (e) pH 5.5 for both soils. All treatments were amended with 50 mg kg-1 glyphosate and incubated at 10 °C, 20 °C or 30 °C. We observed an increase in respiration, microbial biomass and glyphosate mineralization with incubation temperature. Although respiration and microbial biomass in the Humic Cambisol was higher, the microorganisms in the Haplic Chernozem were more active in glyphosate degradation. Increased TOC shifted the microbiome and the 13C-glyphosate degraders towards Gram-positive bacteria in both soils. However, the abundance of 13C-PLFAs indicative for the starvation of Gram-negative bacteria increased with increasing TOC or decreasing pH at higher temperatures. Gram-negative bacteria thus may have been involved in earlier stages of glyphosate degradation.

Impacts of the rhizosphere effect and plant species on organic carbon mineralization rates and pathways, and bacterial community composition in a tidal marsh

Despite the growing recognition regarding the carbon cycle in the rhizosphere of upland ecosystems, little is known regarding the rhizosphere effect on soil organic carbon (SOC) mineralization in tidal marsh soils. In the current study, in situ rhizobox experiments (including rhizosphere and inner and outer bulk soil) were conducted in an estuarine tidal marsh. Our results showed that a higher abundance of total bacteria, Geobacter, dsrA and mcrA and lower α-diversity were observed in the rhizosphere relative to the bulk soil. Rhizosphere effects shifted the partition of terminal metabolic pathways from sulfate reduction in the bulk soil to the co-dominance of microbial Fe(III) and sulfate reduction in the rhizosphere. Although the rhizosphere effect promoted the rates of three terminal metabolic pathways, it showed greater preference towards microbial Fe(III) reduction in the tidal marsh soils. Plant species had little impact on the partitioning of terminal metabolic pathways, but did affect the potential of total SOC mineralization together with the abundance and diversity of total bacteria. Both the rhizosphere effect and plant species influenced the bacterial community composition in the tidal marsh soils; however, plant species had a less pronounced impact on the bacterial community compared with that of the rhizosphere effect.

Insights on comparative bacterial diversity between different arid zones of Cholistan Desert, Pakistan

The present study was conducted to analyze bacterial diversity profile of Cholistan desert located in Pakistan. The study investigates the influence of physicochemical parameters of soil on distribution of different bacteria at all taxonomic levels and also study the distribution pattern between different desert environments, particularly rhizospheric and bulk desert sands. Species richness showed phyla Proteobacteria and Chloroflexi as the dominant OTUs in all the samples. Besides the two phyla, the rhizospheric soils with root remnants were dominated by Firmicutes, Deinococcus-Thermus, Actinobacteria and Acidobacteri, while phylum Thermotogae was present in significant quantity in rhizosheaths devoid of roots. In non-rhizospheric desert soils, a considerable number of OTUs belonged to phyla Proteobacteria, Chloroflexi, Bacteroidetes and Acidobacteria. An important finding from this study is that a bulk portion of the OTUs were assigned to unclassified taxa, indicating a large repertoire of unexplored taxa in the desert ecology of Pakistan. Distribution of taxonomic groups among various regions of the desert was collaborating well with the physicochemical parameters of the sites. The findings of this study establish the fundamental relationships between desert ecosystem, specific native plant and the total bacterial flora. This is the first study of microbial community analysis of any desert in Pakistan and thus, will serve as a future platform to explore further on desert ecosystem functioning by employing the ever-changing biotechnological tools.

Effects of 10 yr of nitrogen and phosphorus fertilization on carbon and nutrient cycling in a tidal freshwater marsh

Tidal freshwater marshes can protect downstream ecosystems from eutrophication by intercepting excess nutrient loads, but recent studies in salt marshes suggest nutrient loading compromises their structural and functional integrity. Here, we present data on changes in plant biomass, microbial biomass and activity, and soil chemistry from plots in a tidal freshwater marsh on the Altamaha River (GA) fertilized for 10 yr with nitrogen (+N), phosphorus (+P), or nitrogen and phosphorus (+NP). Nitrogen alone doubled aboveground biomass and enhanced microbial activity, specifically rates of potential nitrification, denitrification, and methane production measured in laboratory incubations. Phosphorus alone increased soil P and doubled microbial biomass but did not affect microbial processes. Nitrogen or P alone decreased belowground biomass and soil carbon (C) whereas +NP increased aboveground biomass, microbial biomass and N cycling, and N, P, and C assimilation and burial more than either nutrient alone. Our findings suggest differential nutrient limitation of tidal freshwater macrophytes by N and microbes by P, similar to what has been observed in salt marshes. Macrophytes outcompete microbes for P in response to long-term N and P additions, leading to increased soil C storage through increased inputs of belowground biomass relative to N and P added singly. The susceptibility of tidal freshwater marshes to long-term nutrient enrichment and, hence their ability to mitigate eutrophication will depend on the quantity and relative proportion of N vs. P entering estuaries and tidal wetlands.

Stable Isotopes in Greenhouse Gases from Soil: A Review of Theory and Application

Greenhouse gases emitted from soil play a crucial role in the atmospheric environment and global climate change. The theory and technique of detecting stable isotopes in the atmosphere has been widely used to an investigate greenhouse gases from soil. In this paper, we review the current literature on greenhouse gases emitted from soil, including carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). We attempt to synthesize recent advances in the theory and application of stable isotopes in greenhouse gases from soil and discuss future research needs and directions.

The effects of nitrogen addition on dissolved carbon in boreal forest soils of northeastern China

Understanding the effects of nitrogen (N) addition on dissolved carbon in boreal forest soils is essential for accurate evaluation of regional carbon balances. The objective of this study was to determine the effects of different levels and types of N addition on soil dissolved carbon concentration in a cold-temperate coniferous forest through an in-situ fertilization experiment. Simulated atmospheric N addition was applied in a factorial experiment with N addition level (control, 10, 20 and 40 kg of N ha⁻¹yr⁻¹) and N type (NH₄Cl, KNO₃ and NH₄NO₃) treatments. The experiment was conducted over the 2010 growing season (May-September) at the Kailaqi farm of Genhe Forestry Bureau, located in the northern Great Xin’an mountain range, northern China. Monthly N addition treatments were applied in three replicate plots per treatment (n = 36), and measurements of dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) were derived from monthly sampling of the organic and mineral soil horizons. There was a significant effect of N type, with the combined N source (NH₄NO₃) producing significantly higher DOC than the control (ambient addition) or the NH₄Cl treatment in both the organic and mineral layers. The N addition treatment increased DIC in the organic layer at the low levels only, while N type did not have a significant effect. There was a significant interaction of the month and the N level treatment, as low level N addition tended to increase the content of soil DOC while high level N tended to inhibit soil DOC content, with these trends being most pronounced in the middle of the growing season. These results elucidate the importance of the type and timing of N additions to the dynamics of soil carbon pools.

Effect of the amount of organic trigger compounds, nitrogen and soil microbial biomass on the magnitude of priming of soil organic matter

Priming effects (PEs) are defined as short-term changes in the turnover of soil organic matter (SOM) caused by the addition of easily degradable organic compounds to the soil. PEs are ubiquitous but the direction (acceleration or retardation of SOM decomposition) and magnitude are not easy to predict. It has been suggested that the ratio between the amount of added PE-triggering substrate to the size of initial soil microbial biomass is an important factor influencing PEs. However, this is mainly based on comparison of different studies and not on direct experimentation. The aim of the current study is to examine the impact of glucose-to-microbial biomass ratios on PEs for three different ecosystems. We did this by adding three different amounts of ¹³C-glucose with or without addition of mineral N (NH₄NO₃) to soils collected from arable lands, grasslands and forests. The addition of ¹³C-glucose was equivalent to 15%, 50% and 200% of microbial biomass C. After one month of incubation, glucose had induced positive PEs for almost all the treatments, with differences in magnitude related to the soil origin and the amount of glucose added. For arable and forest soils, the primed C increased with increasing amount of glucose added, whereas for grassland soils this relationship was negative. We found positive correlations between glucose-derived C and primed C and the strength of these correlations was different among the three ecosystems considered. Generally, additions of mineral N next to glucose (C:N = 15:1) had little effect on the flux of substrate-derived C and primed C. Overall, our study does not support the hypothesis that the trigger-substrate to microbial biomass ratio can be an important predictor of PEs. Rather our results indicate that the amount of energy obtained from decomposing trigger substrates is an important factor for the magnitude of PEs.

Plant host habitat and root exudates shape fungal diversity

The rhizospheric microbiome is clearly affected by plant species and certain of their functional traits. These functional traits allow plants to adapt to their environmental conditions by acquiring or conserving nutrients, thus defining different ecological resource-use plant strategies. In the present study, we investigated whether plants with one of the two nutrient-use strategies (conservative versus exploitative) could influence fungal communities involved in soil organic matter degradation and root exudate assimilation, as well as those colonizing root tissues. We applied a DNA-based, stable-isotope probing (DNA-SIP) approach to four grass species distributed along a gradient of plant nutrient resource strategies, ranging from conservative to exploitative species, and analyzed their associated mycobiota composition using a fungal internal transcribed spacer (ITS) and Glomeromycotina 18S rRNA gene metabarcoding approach. Our results demonstrated that fungal taxa associated with exploitative and conservative plants could be separated into two general categories according to their location: generalists, which are broadly distributed among plants from each strategy and represent the core mycobiota of soil organic matter degraders, root exudate consumers in the root-adhering soil, and root colonizers; and specialists, which are locally abundant in one species and more specifically involved in soil organic matter degradation or root exudate assimilation on the root-adhering soil and the root tissues. Interestingly, for arbuscular mycorrhizal fungi analysis, all plant roots were mainly colonized by Glomus species, whereas an increased diversity of Glomeromycotina genera was observed for the exploitative plant species Dactylis glomerata.

Potential use of high-throughput sequencing of soil microbial communities for estimating the adverse effects of continuous cropping on ramie (Boehmeria nivea L. Gaud)

Ramie (Boehmeria nivea L. Gaud) fiber, one of the most important natural fibers, is extracted from stem bark. Continuous cropping is the main obstacle to ramie stem growth and a major cause of reduced yields. Root-associated microbes play crucial roles in plant growth and health. In this study, we investigated differences between microbial communities in the soil of healthy and continuously cropped ramie plants, and sought to identify potential mechanisms whereby these communities could counteract the problems posed by continuous cropping. Paired-end Illumina MiSeq analysis of 16S rRNA and ITS gene amplicons was employed to study bacterial and fungal communities. Long-term monoculture of ramie significantly decreased fiber yields and altered soil microbial communities. Our findings revealed how microbial communities and functional diversity varied according to the planting year and plant health status. Soil bacterial diversity increased with the period of ramie monoculture, whereas no significant differences were observed for fungi. Sequence analyses revealed that Firmicutes, Proteobacteria, and Acidobacteria were the most abundant bacterial phyla. Firmicutes abundance decreased with the period of ramie monoculture and correlated positively with the stem length, stem diameter, and fiber yield. The Actinobacteria, Chloroflexi, and Zygomycota phyla exhibited a significant (P < 0.05) negative correlation with yields during continuous cultivation. Some Actinobacteria members showed reduced microbial diversity, which prevented continuous ramie cropping. Ascomycota, Zygomycota, and Basidiomycota were the main fungal phyla. The relatively high abundance of Bacillus observed in healthy ramie may contribute to disease suppression, thereby promoting ramie growth. In summary, soil weakness and increased disease in ramie plants after long-term continuous cropping can be attributed to changes in soil microbes, a reduction in beneficial microbes, and an accumulation of harmful microbes.

Dynamics of microbial biomass and community composition after short-term water status change in Chinese paddy soils

Paddy soil experiences repeated anaerobic and aerobic changes during rice growth, the dramatic dynamics of soil water status accompanied by changes in redox condition and O₂ availability. However, the effect of rapid water status change on soil microbial biomass and community composition is not well explored. Here, we present a comprehensive study focusing on the short-term water status change in 13 Chinese paddy soils. In order to gain a reliable way to determine soil microbial biomass carbon (MBC) in flooded or water-saturated soils, we also evaluated two different procedures (nitrogen bubbled and 100 °C water bath) to remove chloroform in extracts during the fumigation process. Compared to non-flooded paddy soils, the flooded paddy soils tended to have a lower microbial biomass, and this was much clearer using adenosine 5'-triphosphate (ATP) and phospholipid fatty acid (PLFA) analysis compared to biomass measured by the fumigation method. Fungal biomass, which was indicated by both ergosterol and the PLFA 18:2ω6,9c, also decreased after short-term flooding. Changes in soil microbial community composition (determined by PLFA biomarkers) were observed after short-term flooding, but the extent varied between soils. This study indicates that the dynamics of short-term water status altered the soil microbial biomass (ATP, MBC, and total PLFA) and community composition. Finally, our results suggested that liquid fumigation combined with the nitrogen-bubbled method is the best choice for analyzing MBC concentrations in water-saturated soils.

Molecular ecological perspective of methanogenic archaeal community in rice agroecosystem

Methane leads to global warming owing to its warming potential higher than carbon dioxide (CO₂). Rice fields represent the major source of methane (CH₄) emission as the recent estimates range from 34 to 112 Tg CH₄ per year. Biogenic methane is produced by anaerobic methanogenic archaea. Advances in high-throughput sequencing technologies and isolation methodologies enabled investigators to decipher methanogens to be unexpectedly diverse in phylogeny and ecology. Exploring the link between biogeochemical methane cycling and methanogen community dynamics can, therefore, provide a more effective mechanistic understanding of CH₄ emission from rice fields. In this review, we summarize the current knowledge on the diversity and activity of methanogens, factors controlling their ecology, possible interactions between rice plants and methanogens, and their potential involvement in the source relationship of greenhouse gas emissions from rice fields.

Stable isotope probing of carbon flow in the plant holobiont

Microbial communities associated with a plant host, constituting a holobiont, affect the physiology and growth of the plant via metabolites that are mainly derived from their photosynthates. The structure and function of active microbial communities that assimilate root exudates can be tracked by using stable isotope probing (SIP) approaches. This article reviews results from ongoing SIP research in plant-microbe interactions, with a specific focus on investigating the fate of fresh and recalcitrant carbon in the rhizosphere with ¹³C enriched-root exudates, in addition to identifying key players in carbon cycling. Finally, we discuss new SIP applications that have the potential to identify novel enzymes implicated in rhizoremediation or plant genes dedicated to root exudation by combining SIP approaches and genome wide associations studies.

Effect of rice straw application on microbial community and activity in paddy soil under different water status

Rice straw application and flooding are common practices in rice production, both of which can induce changes in the microbial community. This study used soil microcosms to investigate the impact of water status (saturated and nonsaturated) and straw application (10 g kg(-1) soil) on soil microbial composition (phospholipid fatty acid analysis) and activity (MicroResp(™) method). Straw application significantly increased total PLFA amount and individual PLFA components independent of soil moisture level. The amount of soil fungal PLFA was less than Gram-negative, Gram-positive, and actinomycete PLFA, except the drained treatment with rice straw application, which had higher fungal PLFA than actinomycete PLFA at the initial incubation stage. Straw amendment and waterlogging had different effects on microbial community structure and substrate-induced pattern. PLFA profiles were primarily influenced by straw application, whereas soil water status had the greater influence on microbial respiration. Of the variation in PLFA and respiration data, straw accounted for 30.1 and 16.7 %, while soil water status explained 7.5 and 29.1 %, respectively. Our results suggest that (1) the size of microbial communities in paddy soil is more limited by carbon substrate availability rather than by the anaerobic conditions due to waterlogging and (2) that soil water status is more important as a control of fungal growth and microbial community activity.

Microbial Community Structure in the Rhizosphere of Rice Plants

The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth.

A microbial link between elevated CO2 and methane emissions that is plant species-specific

Rising atmospheric CO(2) levels alter the physiology of many plant species, but little is known of changes to root dynamics that may impact soil microbial mediation of greenhouse gas emissions from wetlands. We grew co-occurring wetland plant species that included an invasive reed canary grass (Phalaris arundinacea L.) and a native woolgrass (Scirpus cyperinus L.) in a controlled greenhouse facility under ambient (380 ppm) and elevated atmospheric CO(2) (700 ppm). We hypothesized that elevated atmospheric CO(2) would increase the abundance of both archaeal methanogen and bacterial methanotroph populations through stimulation of plant root and shoot biomass. We found that methane levels emitted from S. cyperinus shoots increased 1.5-fold under elevated CO(2), while no changes in methane levels were detected from P. arundincea. The increase in methane emissions was not explained by enhanced root or shoot growth of S. cyperinus. Principal components analysis of the total phospholipid fatty acid (PLFA) recovered from microbial cell membranes revealed that elevated CO(2) levels shifted the composition of the microbial community under S. cyperinus, while no changes were detected under P. arundinacea. More detailed analysis of microbial abundance showed no impact of elevated CO(2) on a fatty acid indicative of methanotrophic bacteria (18:2ω6c), and no changes were detected in the terminal restriction fragment length polymorphism (T-RFLP) relative abundance profiles of acetate-utilizing archaeal methanogens. Plant carbon depleted in (13)C was traced into the PLFAs of soil microorganisms as a measure of the plant contribution to microbial PLFA. The relative contribution of plant-derived carbon to PLFA carbon was larger in S. cyperinus compared with P. arundinacea in four PLFAs (i14:0, i15:0, a15:0, and 18:1ω9t). The δ(13)C isotopic values indicate that the contribution of plant-derived carbon to microbial lipids could differ in rhizospheres of CO(2)-responsive plant species, such as S. cyperinus in this study. The results from this study show that the CO(2)-methane link found in S. cyperinus can occur without a corresponding change in methanogen and methanotroph relative abundances, but PLFA analysis indicated shifts in the community profile of bacteria and fungi that were unique to rhizospheres under elevated CO(2).

Litter quality as driving factor for plant nutrition via grazing of protozoa on soil microorganisms

Plant residues provide a major source of nitrogen (N) for plant growth. Litter N mineralization varies with litter carbon-to-nitrogen (C-to-N) ratio and presence of bacterial-feeding fauna. We assessed the effect of amoebae, major bacterial feeders in soil, on mineralization of litter of low (high quality) and high C-to-N ratio (low quality) and evaluated consequences for plant growth. We used stable isotopes to determine plant N uptake from litter and plant C partitioning. Stable isotope probing of phospholipid fatty acids was used to follow incorporation of plant C into microorganisms. Amoebae increased plant N uptake independent of litter quality and thereby the biomass of shoots and roots by 33% and 66%, respectively. Plant allocation of total (13)C to roots in low (42%) exceeded that of high-quality litter treatments (26%). Amoebae increased plant allocation of (13)C to roots by 37%. Microbial community structure and incorporation of (13)C into PLFAs varied significantly with litter quality and in the low-quality litter treatment also with the presence of amoebae. Overall, the results suggest that in particular at low nutrient conditions, root-derived C fosters the mobilization of bacterial N by protozoa, thereby increasing plant growth when microorganisms and plants compete for nutrients.

Stable-isotope labeling and probing of recent photosynthates into respired CO2, soil microbes and soil mesofauna using a xylem and phloem stem-injection technique on Sitka spruce (Picea sitchensis)

RATIONALE

Here we report on the successful application of a novel stem-injection stable-isotope-labeling and probing technique in mature trees to trace the spatial and temporal distribution of rhizosphere carbon belowground.

METHODS

Three 22-year-old Sitka spruce trees were injected with 6.66 g of (13)C-labeled aspartic acid. Over the succeeding 30 days, soil CO(2) efflux, phospholipid fatty-acid (PLFA) microbial biomarkers and soil invertebrates (mites, collembolans and enchytraeids) were analyzed along a 50 m transect from each tree to determine the temporal and spatial patterns in the translocation of recently fixed photosynthates belowground.

RESULTS

Soil δ(13)CO(2) values peaked 13-23 days after injection, up to 5 m from the base of the injected tree and was, on average, 3.5‰ enriched in (13)C relative to the baseline. Fungal PLFA biomarkers peaked 2-4 days after stem-injection, up to 20 m from the base of the injected tree and were (13)C-enriched by up to 50‰. Significant (13)C enrichment in mites and enchytraeids occurred 4-6 days after injection (by, on average, 1.5‰).

CONCLUSIONS

Stem injection of large trees with (13)C-enriched compounds is a successful tool to trace C-translocation belowground. In particular, the significant (13)C enrichment of CO(2) and enchytraeids near the base of the tree and the significant (13)C enrichment of PLFAs up to 20 m away indicate that mature Sitka spruce (Picea sitchensis) have the capacity to support soil communities over large distances.

13C pulse-labeling assessment of the community structure of active fungi in the rhizosphere of a genetically starch-modified potato (Solanum tuberosum) cultivar and its parental isoline

• The aim of this study was to gain understanding of the carbon flow from the roots of a genetically modified (GM) amylopectin-accumulating potato (Solanum tuberosum) cultivar and its parental isoline to the soil fungal community using stable isotope probing (SIP). • The microbes receiving (13)C from the plant were assessed through RNA/phospholipid fatty acid analysis with stable isotope probing (PLFA-SIP) at three time-points (1, 5 and 12 d after the start of labeling). The communities of Ascomycota, Basidiomycota and Glomeromycota were analysed separately with RT-qPCR and terminal restriction fragment length polymorphism (T-RFLP). • Ascomycetes and glomeromycetes received carbon from the plant as early as 1 and 5 d after labeling, while basidiomycetes were slower in accumulating the labeled carbon. The rate of carbon allocation in the GM variety differed from that in its parental variety, thereby affecting soil fungal communities. • We conclude that both saprotrophic and mycorrhizal fungi rapidly metabolize organic substrates flowing from the root into the rhizosphere, that there are large differences in utilization of root-derived compounds at a lower phylogenetic level within investigated fungal phyla, and that active communities in the rhizosphere differ between the GM plant and its parental cultivar through effects of differential carbon flow from the plant.

Effects of genetically modified starch metabolism in potato plants on photosynthate fluxes into the rhizosphere and on microbial degraders of root exudates

A high percentage of photosynthetically assimilated carbon is released into soil via root exudates, which are acknowledged as the most important factor for the development of microbial rhizosphere communities. As quality and quantity of root exudates are dependent on plant genotype, the genetic engineering of plants might also influence carbon partitioning within the plant and thus microbial rhizosphere community structure. In this study, the carbon allocation patterns within the plant-rhizosphere system of a genetically modified amylopectin-accumulating potato line (Solanum tuberosum L.) were linked to microbial degraders of root exudates under greenhouse conditions, using (13)C-CO(2) pulse-chase labelling in combination with phospholipid fatty acid (PLFA) analysis. In addition, GM plants were compared with the parental cultivar as well as a second potato cultivar obtained by classical breeding. Rhizosphere samples were obtained during young leaf developmental and flowering stages. (13)C allocation in aboveground plant biomass, water-extractable organic carbon, microbial biomass carbon and PLFA as well as the microbial community structure in the rhizosphere varied significantly between the natural potato cultivars. However, no differences between the GM line and its parental cultivar were observed. Besides the considerable impact of plant cultivar, the plant developmental stage affected carbon partitioning via the plant into the rhizosphere and, subsequently, microbial communities involved in the transformation of root exudates.

Low amounts of herbivory by root-knot nematodes affect microbial community dynamics and carbon allocation in the rhizosphere

Increased carbon translocation to the rhizosphere via 'leakage' induced by low amounts of plant parasitic nematodes can foster microorganisms. The effects of the root-knot nematode Meloidogyne incognita on microbial biomass (C(mic)) and community structure (phospholipid fatty acids) in the rhizosphere of barley were studied. Inoculation densities of 2000, 4000, and 8000 nematodes were well below the threshold level for plant damage. A (13)CO(2) pulse-labelling was performed to assess the distribution of assimilated (13)C in the rhizosphere. Infection with M. incognita increased the carbon concentration in shoots, and enhanced root biomass slightly. The presence of nematodes did not affect microbial biomass, but significantly changed the allocation of the recent photosynthate. Less plant carbon was sequestered by microorganisms with increasing nematode abundance. Microbial community structure was distinctly altered in the early stages of the plant-nematode interactions. Both, bacteria and fungi, showed a positive response with 2000, and a negative one with 4000 and 8000 M. incognita added. The results suggest that low-level root herbivory still imposes a considerable carbon demand, and that proliferation of microorganisms due to increased rhizodeposition may be short-termed. The carbon flow to rhizosphere microbial communities is likely dependent on the specific nematode-plant association and the developmental stage of the nematode in the host.

Spatial variation of active microbiota in the rice rhizosphere revealed by in situ stable isotope probing of phospholipid fatty acids

This report is part of a serial study applying stable isotope labelling to rice microcosms to track the utilization of recently photosynthesized carbon by active microbiota in the rhizosphere. The objective of the present study was to apply phospholipid fatty acid-based stable isotope probing (PLFA-SIP) to detect the spatial variation of active microorganisms associated with rhizosphere carbon flow. In total, 49 pulses of 13CO2 were applied to rice plants in a microcosm over a period of 7 days. Rhizosphere soil was separated from bulk soil by a root bag. Soil samples were taken from rhizosphere and bulk soil, and the bulk soil samples were further partitioned both vertically (up layer and down layer) and horizontally with increasing distance to the root bag. Incorporation of 13C into PLFAs sharply decreased with distance to the roots. The labelling of 16:1omega9, 18:1omega7, 18:1omega9, 18:2omega6,9 and i14:0 PLFAs was relatively stronger in the rhizosphere while that of i15:0 and i17:0 increased in the bulk soil. The microorganisms associated with 16:1omega9 were active in both up- and down-layer soils. The microorganisms represented by i14:0, 18:1omega7 and 18:2omega6,9 exhibited a relatively higher activity in up-layer soil, whereas those represented by i15:0 and i17:0 were more active in down-layer soil. These results suggest that in the rhizosphere Gram-negative and eukaryotic microorganisms were most actively assimilating root-derived C, whereas Gram-positive microorganisms became relatively more important in the bulk soil. The active populations apparently differed between up- and down-layer soil and in particular changed with distance to the roots, demonstrating systematic changes in the activity of the soil microbiota surrounding roots.

Structure and activity of bacterial community inhabiting rice roots and the rhizosphere

Root-derived carbon provides a major source for microbial production and emission of CH4 from rice field soils. Therefore, we characterized the structure and activity of the bacterial community inhabiting rice roots and the rhizosphere. In the first experiment, DNA retrieved from rice roots was analysed for bacterial 16S rRNA genes using cloning, sequencing and in situ hybridization. In the second experiment, rice plants were pulse-labelled with 13CO2 (99% of atom 13C) for 7 days, and the bacterial RNA was isolated from rhizosphere soil and subjected to density gradient centrifugation. RNA samples from density fractions were analysed by terminal restriction fragment length polymorphism fingerprinting, cloning and sequencing. The experiments showed that the dominant bacteria inhabiting rice roots and the rhizosphere particularly belonged to the Alphaproteobacteria, Betaproteobacteria and Firmicutes. The RNA stable isotope probing revealed that the bacteria actively assimilating C derived from the pulse-labelled rice plants were Azospirillum spp. (Alphaproteobacteria) and members of Burkholderiaceae (Betaproteobacteria). Both anaerobic (e.g. Clostridia) and aerobic (e.g. Comamonas) degraders were present at high abundance, indicating that root environments and degradation processes were highly heterogeneous. The relative importance of iron and sulfate reducers suggested that cycling of iron and sulfur is active in the rhizosphere.

13C-Labelling of lipids to investigate microbial communities in the environment

The introduction of (13)C-labelled substrates to soils, sediments or cultures followed by (13)C analysis of phospholipid fatty acids (PLFAs) provides quantitative and chemotaxonomic information for the groups of microorganisms utilizing a given substrate. Gas chromatography-combustion-isotope ratio mass spectrometry has provided the high precision necessary to measure small isotopic changes (differences in the relative abundances of (13)C to (12)C expressed as delta(13)C values) for nanogram amounts of individual compounds, such as microbial PLFAs. This methodology constitutes a powerful new culture-independent method for investigating microbial communities in the environment. The information obtained is highly complementary to that obtained from gene-probe-based methods, and considerable possibilities exist to extend this methodology to include other biochemical components of microorganisms.

Studying plant-microbe interactions using stable isotope technologies

Interactions between plants and microorganisms in the rhizosphere are complex and varied. They include the general transfer of nutrients and specific interactions mediated by the release of signalling molecules from plant roots. Until recently, understanding the nature of these interactions was limited by a reliance on traditional, cultivation-based techniques. Stable isotope probing provides the potential for cultivation-independent characterisation of organisms actively assimilating carbon derived from plant root exudate or added to the soil. Current applications have focused on interactions with relatively low-level specificity, but there is significant potential for mechanistic studies of more specific interactions, particularly if the sensitivity of the technique can be increased.

Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community

The goal of this field study was to provide insight into three distinct populations of microorganisms involved in in situ metabolism of phenol. Our approach measured 13CO2 respired from [13C]phenol and stable isotope probing (SIP) of soil DNA at an agricultural field site. Traditionally, SIP-based investigations have been subject to the uncertainties posed by carbon cross-feeding. By altering our field-based, substrate-dosing methodologies, experiments were designed to look beyond primary degraders to detect trophically related populations in the food chain. Using gas chromatography-mass spectrometry (GC/MS), it was shown that (13)C-labeled biomass, derived from primary phenol degraders in soil, was a suitable growth substrate for other members of the soil microbial community. Next, three dosing regimes were designed to examine active members of the microbial community involved in phenol metabolism in situ: (i) 1 dose of [13C]phenol, (ii) 11 daily doses of unlabeled phenol followed by 1 dose of [13C]phenol, and (iii) 12 daily doses of [13C]phenol. GC/MS analysis demonstrated that prior exposure to phenol boosted 13CO2 evolution by a factor of 10. Furthermore, imaging of 13C-treated soil using secondary ion mass spectrometry (SIMS) verified that individual bacteria incorporated 13C into their biomass. PCR amplification and 16S rRNA gene sequencing of 13C-labeled soil DNA from the 3 dosing regimes revealed three distinct clone libraries: (i) unenriched, primary phenol degraders were most diverse, consisting of alpha-, beta-, and gamma-proteobacteria and high-G+C-content gram-positive bacteria, (ii) enriched primary phenol degraders were dominated by members of the genera Kocuria and Staphylococcus, and (iii) trophically related (carbon cross-feeders) were dominated by members of the genus Pseudomonas. These data show that SIP has the potential to document population shifts caused by substrate preexposure and to follow the flow of carbon through terrestrial microbial food chains.

In Situ Stable Isotope Probing of Methanogenic Archaea in the Rice Rhizosphere

Microorganisms living in anoxic rice soils contribute 10 to 25% of global methane emissions. The most important carbon source for CH4 production is plant-derived carbon that enters soil as root exudates and debris. Pulse labeling of rice plants with 13CO2 resulted in incorporation of 13C into the ribosomal RNA of Rice Cluster I Archaea in the soil, indicating that this archaeal group plays a key role in CH4 production from plant-derived carbon. This group of microorganisms has not yet been isolated but appears to be of global environmental importance.