Metabolic Diversity Of Microbial Communities Research Articles

Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings

The microbial guild coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is an innovative process to achieve energy-efficient nitrogen removal with the beneficial use of methane in biogas or in anaerobically treated wastewater. Here, metagenomics and metatranscriptomics were used to reveal the microbial ecology of two biofilm systems, which incorporate anammox and n-DAMO for high-level nitrogen removal in low-strength domestic sewage and high-strength sidestream wastewater, respectively. We find that different nitrogen loadings (i.e., 0.1 vs. 1.0 kg N/m3/d) lead to different combinations of anammox bacteria and anaerobic methanotrophs (“Candidatus Methanoperedens” and “Candidatus Methylomirabilis”), which play primary roles for carbon and nitrogen transformations therein. Despite methane being the only exogenous organic carbon supplied, heterotrophic populations (e.g., Verrucomicrobiota and Bacteroidota) co-exist and actively perform partial denitrification or dissimilatory nitrate reduction to ammonium (DNRA), likely using organic intermediates from the breakdown of methane and biomass as carbon sources. More importantly, two novel genomes belonging to “Ca. Methylomirabilis” are recovered, while one surprisingly expresses nitrate reductases, which we designate as “Ca. Methylomirabilis nitratireducens” representing its inferred capability in performing nitrate-dependent anaerobic methane oxidation. This finding not only suggests a previously neglected possibility of “Ca. Methylomirabilis” bacteria in performing methane-dependent nitrate reduction, and also challenges the previous understanding that the methane-dependent complete denitrification from nitrate to dinitrogen gas is carried out by the consortium of bacteria and archaea.

Spatial variation and metabolic diversity of microbial communities in the surface sediments of the Mariana Trench.

Mariana Trench represents the deepest and one of least explored biosphere on Earth, and its carbon sources include euphotic sinking, lateral transportation and diffusion from underlying crust, etc. By far the spatial variation of microbial community with associated organic carbon degradation potential in the surface sediments of the Mariana Trench were still largely unknown. Based on the high-throughput 16S rRNA amplicon sequencing, significantly different microbial community structure was overserved between the shallow (<10,000 m) and deep stations (>10,000 m), which could be explained by spatial variation of Chloroflexi, Proteobacteria and Crenarchaeota, with sampling depth and total organic carbon (TOC) content as the environmental driving forces. During the 109-day incubation with Biolog EcoPlate™ microplate, polymers and carbohydrates were preferentially used, followed by amino acids and carboxylic acids, and microbial metabolic diversity was significantly different between the shallow and deep stations. The metabolic diversity of microorganisms at most shallow stations was significantly lower than that at deep stations. This could potentially be attributed the metabolic capabilities of different microbial groups with varied ecological niches, and reflected the initial preference of carbon source by the nature microbes as well. Our study obtained a rough assessment of physiological and taxonomic characteristics of the trench sediment microbial community with polyphasic approaches. Distinct microbial structure and potential carbon metabolic functions in different sampling depths might led to the differentiation of ecological niches, which enable various microorganisms to make full use of the limited resources in the deep sea, and provided a research basis for further exploration of the carbon cycle in different deep-sea regions.

Effects of crop production practices on soil characteristics and metabolic diversity of microbial communities under winter wheat

The aim of this research was to compare the effects of organic (ORG, no mineral fertilisers and pesticides) and conventional (CON, with mineral fertilisation and plant protection chemicals) crop production systems on some soil properties: soil organic matter (SOM) and particulate organic matter (POM) contents, dehydrogenase activity and metabolic microbial diversity (Biolog EcoPlate™). Samples of Haplic Luvisol soil were collected from 23-year-old experimental fields under winter wheat from the depth layers of 0–5, 5–10, 15–20 and 30–35cm. Soil under ORG showed higher contents of SOM, POM and POM expressed as a percentage of SOM by 16.0%, 25.6% and 23.9% respectively, in particular down to 5cm depth, compared with the CON system. Also, dehydrogenase activity was 47.5% higher under the ORG than the CON system. The Biolog EcoPlate revealed higher metabolic microbial diversity in soil under ORG crop production system compared with CON. This result was supported by the average well colour development and Shannon’s diversity index values. Significant correlations between soil quality parameters and winter wheat yield confirmed their effectiveness as indicators of soil disturbance. The results showed that the ORG system much better maintained SOM and soil fertility compared with CON.

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.

Genome-scale metabolic models derived from human gut metagenomic data can be used as a framework to elucidate how microbial communities modulate human metabolism and health. We present AGORA (assembly of gut organisms through reconstruction and analysis), a resource of genome-scale metabolic reconstructions semi-automatically generated for 773 human gut bacteria. Using this resource, we identified a defined growth medium for Bacteroides caccae ATCC 34185. We also showed that interactions among modeled species depend on both the metabolic potential of each species and the nutrients available. AGORA reconstructions can integrate either metagenomic or 16S rRNA sequencing data sets to infer the metabolic diversity of microbial communities. AGORA reconstructions could provide a starting point for the generation of high-quality, manually curated metabolic reconstructions. AGORA is fully compatible with Recon 2, a comprehensive metabolic reconstruction of human metabolism, which will facilitate studies of host-microbiome interactions.

Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria.

Genome sequencing has revealed that horizontal gene transfer (HGT) is a major evolutionary process in bacteria. Although it is generally assumed that closely related organisms engage in genetic exchange more frequently than distantly related ones, the frequency of HGT among distantly related organisms and the effect of ecological relatedness on the frequency has not been rigorously assessed. Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. Our analysis revealed the existence of networks of genetic exchange between organisms with overlapping ecological niches, with mesophilic anaerobic organisms showing the highest frequency of exchange and engaging in HGT twice as frequently as their aerobic counterparts. Examination of individual cases suggested that inter-phylum HGT is more pronounced than previously thought, affecting up to ∼ 16% of the total genes and ∼ 35% of the metabolic genes in some genomes (conservative estimation). In contrast, ribosomal and other universal protein-coding genes were subjected to HGT at least 150 times less frequently than genes encoding the most promiscuous metabolic functions (for example, various dehydrogenases and ABC transport systems), suggesting that the species tree based on the former genes may be reliable. These results indicated that the metabolic diversity of microbial communities within most habitats has been largely assembled from preexisting genetic diversity through HGT and that HGT accounts for the functional redundancy among phyla.

Plant roots influence microbial activities as well as cadmium and zinc fractions in metal-contaminated soil

Changes in soil pH, soil heavy metal forms, and the metabolic diversity of microbial communities were examined in soil samples collected in 1-mm increments from barley roots in soil contaminated with cadmium (Cd) and zinc (Zn) using a rhizobox system. Concentrations of exchangeable Cd and Zn increased near the roots owing to a decrease in soil pH. Conversely, the concentration of inorganically bound Cd and Zn decreased near the roots. Despite having the highest concentration of the most toxic exchangeable metals, the rhizosphere also had the highest bacterial and fungal metabolic activity and diversity when assessed using BIOLOG plates. Therefore, the promoting effects of root exudates on microbial activity could outweigh the adverse effects of Cd and Zn on microorganisms in the rhizosphere.

The influence of winter wheat continuous cropping and fertilization on the crop yields and microbial soil diversity

The possibilities of the elimination of continuous cropping negative implications on the grain yield and microbial soil diversity were investigated. A stationary field experiment was established on Luvi-Haplic Chernozem. Statistically higher grain yield was found in the variant with mineral fertilization and straw and organic fertiliser Veget® incorporation (5.58 t.ha−1) compared with the variant with mineral fertilization only (4.87 t.ha−1) and with the variant with mineral fertilization and straw incorporation (4.90 t.ha−1). Statistically higher straw yield was found in the variant with mineral fertilization and straw and organic fertiliser Veget® incorporation (6.21 t.ha−1) compared with the variant with mineral fertilization only (4.41 t.ha−1). By cultivar Ebi, the grain yield was significantly higher in comparison to the cultivar Petrana. The lowest metabolic diversity of microbial communities and their respiration activity was found out in the variant with mineral fertilizer. On the other hand, the increase of functional diversity of microorganisms, their respiration activity and the number of cultivable bacteria was found in the variant with mineral fertilization and straw incorporation as well as in the variant with mineral fertilization and straw and organic fertiliser Veget® incorporation.

Molecular identification of rumen methanogens: Technologies, advances and prospects

Methanogenesis provides a means of H2 disposal and a mechanism to maintain low partial H2 pressure in the rumen, a prerequisite for efficient ruminal fermentation. As methanogens possess stringent requirements for cultivation, only a few species have been successfully isolated from the rumen and cultured. Culture independent molecular based approaches have provided new insight into the diversity, prevalence and role of methanogens within the overall rumen microbial community. In addition, recent developments in next generation sequencing technology have enabled the ruminal microbial community to be investigated at a metagenomic level, providing information to explore the structure, function and metabolic diversity of microbial communities. This review summarizes existing molecular technologies utilized in studies of ruminal methanogens by outlining their advantages and limitations, and introduces future applications of next generation sequencing approaches for studying the ecology of ruminal methanogens. These approaches could provide new understanding of the mechanisms of methanogenesis, as well as interactions of methanogens with other members of the rumen microbial community. An understanding of the fundamental role of methanogens in ruminal CH4 production would provide insight into methods of curtailing emissions of this greenhouse gas from ruminants.This article is part of the special issue entitled: Greenhouse Gases in Animal Agriculture – Finding a Balance between Food and Emissions, Guest Edited by T.A. McAllister, Section Guest Editors; K.A. Beauchemin, X. Hao, S. McGinn and Editor for Animal Feed Science and Technology, P.H. Robinson.

Iron and carbon isotope evidence for ecosystem and environmental diversity in the ∼2.7 to 2.5Ga Hamersley Province, Western Australia

The largest excursion in kerogen δ13C and bulk/mineral δ56Fe values yet measured in the ancient rock record occurs in rocks of ∼ 2.7 to 2.5 Ga age. New Fe isotope data integrated with previously collected C isotope data on the same samples document the metabolic diversity of microbial communities in the Neoarchean Hamersley Province of the Pilbara Craton in Western Australia. Samples of shales, carbonates, and mixed carbonate/shale lithologies were collected from three drill cores; two cores from the depocenter of the province and one from the margin. Shallow-water clastic/carbonate rocks deposited in the center of the province (Tumbiana Formation) record kerogen δ13C values that indicate C cycling by various anaerobic or aerobic methane pathways, but the restricted range in δ56Fe values indicates little or no Fe redox cycling. Deep-water sediments deposited contemporaneously in both parts of the Hamersley Province (Jeerinah Formation) record slightly positive δ56Fe values in the relatively shallower and suboxic margin, but strongly negative δ56Fe values in the deeper euxinic depocenter of the province, a pattern consistent with Fe cycling via a basin Fe shuttle, driven by bacterial dissimilatory iron reduction (DIR). Kerogen δ13C values from these units indicate coupling of microbial Fe cycling to aerobic methanotrophy or anaerobic oxidation of methane. Younger black shales, intercalated with iron formation (Marra Mamba Iron Formation) in the depocenter, record a shift to near-zero δ56Fe values reflecting an Fe budget dominated by hydrothermal and clastic sources. However, time-equivalent, Fe-rich carbonate/shale lithologies deposited on the margin of the province (Carawine Dolomite) have δ56Fe values that steadily decrease from near zero to strongly negative values. These relatively Fe-rich carbonates may reflect a carbonate trap of a DIR-driven Fe shuttle, similar to the sulfidic trap in the euxinic portion of the Jeerinah Formation. In contrast, younger shallow-water carbonates deposited by turbidity currents in relatively deep water in the center of the province (Wittenoom Formation), have δ56Fe values that correlate with Fe concentrations, a pattern that indicates Fe cycling by Rayleigh fractionation through precipitation of iron oxides from aqueous ferrous iron.

Achievements and new knowledge unraveled by metagenomic approaches

Metagenomics has paved the way for cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. In recent years, significant progress has been made in this research area. A major breakthrough was the improvement and development of high-throughput next-generation sequencing technologies. The application of these technologies resulted in the generation of large datasets derived from various environments such as soil and ocean water. The analyses of these datasets opened a window into the enormous phylogenetic and metabolic diversity of microbial communities living in a variety of ecosystems. In this way, structure, functions, and interactions of microbial communities were elucidated. Metagenomics has proven to be a powerful tool for the recovery of novel biomolecules. In most cases, functional metagenomics comprising construction and screening of complex metagenomic DNA libraries has been applied to isolate new enzymes and drugs of industrial importance. For this purpose, several novel and improved screening strategies that allow efficient screening of large collections of clones harboring metagenomes have been introduced.

Evaluation of the metabolic diversity of microbial communities in four different filter layers of a constructed wetland with vertical flow by Biolog™ analysis

The community-level substrate utilization test based on direct incubation of environmental samples in Biolog EcoPlates™ is a suitable and sensitive tool to characterize microbial communities. The aim of this study was to investigate the influence of plant roots and soil structure on the metabolic diversity of microorganisms in a constructed wetland with vertical flow. Sediment samples were taken from different filter depths representing specific filter layers. The color development representing the substrate utilization was measured with the samples over a period of 10 days. The average well color development (AWCD) for all carbon sources was calculated as an indicator of total activity and in order to compensate the influence of the inoculum's density on the color development in the plates. After transformation by dividing by the AWCD, the optical density data were analysed by principal component analysis (PCA). An analysis of the kinetic profile of the AWCD was carried out to increase the analytical power of the method. The corrected data have been successfully fit to the logistic growth equation. Three kinetic model parameters, the asymptote ( K), the exponential rate of color change ( p) and the time to the midpoint of the exponential portion of the curve ( s), were used for statistical analysis of the physiological profile of the microbial community in the different filter layers of the constructed wetland. We found out that in the upper two horizons, which were rooted most densely, mainly easily degradable materials like specific carbohydrates were utilized, while in the lower layers, where only single roots occur, more biochemically inert compounds, e.g. 2-hydroxy benzoic acid, were utilized. Furthermore it could be shown that microorganisms in the surface layer benefited from the plant litter because they can utilize decay products of these. In the lower filter layers specialists took advantage because they had to cope with the biochemically inert materials and the lower nutrient supply.

GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent

Deep-sea hydrothermal vents are one of the most unique and fascinating ecosystems on Earth. Although phylogenetic diversity of vent communities has been extensively examined, their physiological diversity is poorly understood. In this study, a GeoChip-based, high-throughput metagenomics technology revealed dramatic differences in microbial metabolic functions in a newly grown protochimney (inner section, Proto-I; outer section, Proto-O) and the outer section of a mature chimney (4143-1) at the Juan de Fuca Ridge. Very limited numbers of functional genes were detected in Proto-I (113 genes), whereas much higher numbers of genes were detected in Proto-O (504 genes) and 4143-1 (5,414 genes). Microbial functional genes/populations in Proto-O and Proto-I were substantially different (around 1% common genes), suggesting a rapid change in the microbial community composition during the growth of the chimney. Previously retrieved cbbL and cbbM genes involved in the Calvin Benson Bassham (CBB) cycle from deep-sea hydrothermal vents were predominant in Proto-O and 4143-1, whereas photosynthetic green-like cbbL genes were the major components in Proto-I. In addition, genes involved in methanogenesis, aerobic and anaerobic methane oxidation (e.g., ANME1 and ANME2), nitrification, denitrification, sulfate reduction, degradation of complex carbon substrates, and metal resistance were also detected. Clone libraries supported the GeoChip results but were less effective than the microarray in delineating microbial populations of low biomass. Overall, these results suggest that the hydrothermal microbial communities are metabolically and physiologically highly diverse, and the communities appear to be undergoing rapid dynamic succession and adaptation in response to the steep temperature and chemical gradients across the chimney.

Microbial biomass and growth kinetics of microorganisms in chernozem soils under different land use modes

The carbon content of microbial biomass and the kinetic characteristics of microbial respiration response to substrate introduction have been estimated for chernozem soils of different farm lands: arable lands used for 10, 46, and 76 years, mowed fallow land, non-mowed fallow land, and woodland. Microbial biomass and the content of microbial carbon in humus (Cmic/Corg) decreased in the following order: soils under forest cenoses-mowed fallow land-10-year arable land-46- and 75-year arable land. The amount of microbial carbon in the long-plowed horizon was 40% of its content in the upper horizon of non-mowed fallow land. Arable soils were characterized by a lower metabolic diversity of microbial community and by the highest portion of microorganisms able to grow directly on glucose introduced into soil. The effects of different scenarios of carbon sequestration in soil on the reserves and activity of microbial biomass are discussed.

16S rDNA analysis reveals low microbial diversity in community level physiological profile assays

The metabolic diversity of microbial communities is fundamental for the multiple soil functions mediated by microorganisms. Community level physiological profiles (CLPPs) based on sole C source oxidation have been used as a fast and reproducible tool to study soil microbial functional diversity because the utilisation of available carbon is the key factor governing microbial growth in soil. Our aim was to assess the phylogenetic affiliation of the microorganisms responsible for C consumption after inoculating Biolog™ plates. For this purpose, two semi-arid Mediterranean forest soils with significantly different patterns of C consumption and microbial community structure were used. Following the inoculation of the Biolog plates, suspensions from seven wells were sampled after 1, 2 and 7 d of incubation. DNA was extracted and the microbial communities analysed by polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR–DGGE) and sequencing of excised bands.Despite major differences in the microbial communities of the soils studied, their DGGE banding patterns after incubation were similar for all the analysed C source suspensions. Microorganisms belonging to β-Proteobacteria (Ralstonia sp. and Burkholderia sp.) and α-Proteobacteria (Rhizobium sp.) were dominant. These opportunists had a competitive advantage under the conditions at which the CLPPs were analysed.This study reveals that significantly different CLPP patterns can be generated on the basis of only 3–4 genera, as reflected by PCR–DGGE analysis. Also for this reason, CLPPs based on incubations of soil suspensions should just be used as a screening method and always be accompanied by other techniques for community analysis.

Changes in microbial biomass and microbial activity of pig slurry after the transit through the gut of the earthworm Eudrilus eugeniae (Kinberg, 1867)

Here we studied the effects of gut transit through the earthworm Eudrilus eugeniae, on the physicochemical, biochemical, and microbial characteristics of pig slurry, by analyzing fresh casts. The reduction in the dissolved organic C contents in casts we recorded suggests that during digestion, earthworms assimilated labile organic C preferentially, which is a limiting growth factor for them. Furthermore, both microbial biomass and activity in pig slurry were significantly decreased by earthworm gut transit. It appears that E. eugeniae is able to digest microorganisms, although the addition of glucose to the food increased respiration, indicating that growth of microorganisms in casts could be limited by depletion of labile C. Despite reduced microbial biomass and activity, the metabolic diversity of microbial communities was greater in casts than in original pig slurry. Community level physiological profiles obtained from Biolog Ecoplate data revealed that, after earthworm gut transit, the microbial communities in casts and pig slurry were clearly differentiated by their physiological profiles. The results indicate that first stage in vermicomposting of pig slurry by E. eugeniae, i.e., casting, produced changes that will influence the dynamics of the organic matter degradation by reducing forms of N and C available to microorganisms, hence restricting their growth and multiplication. Nevertheless, the reduced microflora of casts was characterized by an increased catabolic potential that might lead to thorough degradation of pig slurry.

Properties and metabolic diversity of microbial communities in soils treated with steam sterilization compared with methyl bromide and chloropicrin fumigations

The effects of steam sterilization (SS) on soil microbial properties including metabolic diversity of the microbial communities were examined in a greenhouse compared with those of two fumigants, methyl bromide (MB) and chloropicrin (CP). The numbers of fungi decreased in all the treatments. Nitrifiers, both ammonium-oxidizing bacteria and nitrite-oxidizing bacteria, were severely affected by the SS and CP treatments, resulting in their virtual disappearance. The decrease in the levels of microbial biomass C and N after the treatments suggested that the SS and CP treatments eradicated the microorganisms more effectively than the MB treatment and that the influence of the former persisted until the end of the experiment, 4 months after the treatments. Accumulation of NH4-N was observed after the SS and CP treatments mainly due to the partial decomposition of the dead microorganisms and the marked decrease in the number of ammonium-oxidizing bacteria. The richness and average well color development (AWCD) values in the microbial communities after the SS treatment were evaluated by the carbon substrate utilization method using Biolog ECO MicroPlates. The values decreased markedly immediately after the treatment but showed a rapid recovery, while those after the CP treatment continued to decrease until the transplanting of tomato seedlings. The effect of the MB treatment on the soil microbial communities was less pronounced. The growth of the tomato plants was promoted by the SS and CP treatments due to the increase in the N supply at the initial stage of tomato growth.

Rhizosphere Microbial Characterization in Petroleum-Contaminated Soil

Contamination of soil with petroleum compounds is of concern worldwide. Although there are a variety of physical and chemical technologies available to remediate petroleum waste sites, biological methods are often used due to lower cost and public acceptance. Growth and enhanced activity of microbial communities in contaminated soil is a key factor for the success of bioremediation. Establishing vegetation in petroleum-contaminated soil may enhance microbial activity and remediation success even further by providing root exudates to the rhizosphere microorganisms. In this study, microorganisms were characterized in petroleum-contaminated soils and sediments quantitatively and qualitatively based on enumeration and metabolic diversity assessments. Contaminated soils and sediments were obtained from a phytoremediation field demonstration project in California. Microbial numbers in the unvegetated soil, based on plate counts and most probable number of hydrocarbon degraders, were significantly lower than the vegetated soils. Metabolic microbial characterization using BIOLOG was also conducted and based on principle component analysis (PCA), there was a distinct difference between the metabolic diversity of microbial communities in vegetated and unvegetated soils. Results from this research indicate that the presence and type of plants, and level of contamination may greatly influence microbial communities in polluted soils.

The Impact of Oxygen Tension on Cell Density and Metabolic Diversity of Microbial Communities in Alkane Degrading Continuous-Flow Cultures.

Abstract The impact of the dissolved O2 tension (DOT) and the dilution rate on the metabolic diversity of an autochthonous hexadecane-degrading community in continuous-flow cultures containing hexadecane-coated intertidal sediment was determined in a set of experiments. The DOT was kept constant within each culture at values of 80% (168 µmol O2L-1) or 0.4% (0.84 µmol O2 L-1). The dilution rate was increased from D = 0.012 h-1 to D = 0.06 h-1. To determine the culture activity, we analyzed the hexadecane degradation rate, the protein production rate, and the oxygen consumption rate. The cell concentration of different metabolic groups was determined by colony forming units (CFU), and by most probable number (MPN). The metabolic diversity was determined by the substrate utilization spectrum in Biolog GN microtiter plates. The substrate utilization pattern of the cultures decreased considerably as D increased. This effect was more pronounced at 0.4% of DOT than at 80% of DOT. The MPN and CFU revealed that as D increased, only minor changes occurred in the community structure. The hexadecane degradation rate, the protein production rate, and the oxygen consumption rate increased parallel to D independently of the DOT. This means that the biocenosis at 0.4% of DOT was different from the biocenosis at 80% of DOT, although the metabolic activity of the cultures was unaffected by a 200-factor difference in the oxygen tension and revealed a considerable buffer capacity with respect to changes in DOT.

Impact of elevated CO(2) on the metabolic diversity of microbial communities in N-limited grass swards

The impact of elevated atmospheric CO2 on qualitative and qua ntitative changes in rhizosphere carbon flow will have important consequences fo r nutrient cycling and storage in soil, through the effect on the activity, biom ass size and composition of soil microbial communities. We hypothesized that mic robial communities from the rhizosphere of Danthonia richardsonii, a n ative C3 Australian grass, growing at ambient and twice ambient CO2 a nd varying rates of low N application (20, 60, 180 kg N ha-1) will be different as a consequence of qualitative and quantitative change in rhizosphere carbon flow. We used the BiologTM system to construct sole carbon source utilisation profiles of these communities from the rhizosphere of D. richardsonii. BiologTM GN and MT plates, the latter to which more ecologically relevant root exudate carbon sources were added, were used to characterise the communities. Microbial communities from the rhizosphere of D. richardsonii grown for four years at twice ambient CO2 had significantly greater utilisation of all carbon sources except those with a low C:N ratio (neutral and acidic amino acids, amides, N-heterocycles, long chain aliphatic acids) than communities from plants grown at ambient CO2. This indicates a change in microbial community composition suggesting that under elevated CO2 compounds with a higher C:N ratio were exuded. Enumeration of microorganisms, using plate counts, indicated that there was a preferential stimulation of fungal growth at elevated CO2 and confirmed that bacterial metabolic activity (C utilisation rates), not population size (counts), were stimulated by additional C flow at elevated CO2. Nitrogen was an additional rate-limiting factor for microbial growth in soil and had a significant impact on the microbial response to elevated CO2. Microbial populations were higher in the rhizosphere of plants receiving the highest N application, but the communities receiving the lowest N application were most active. These results have important implications for carbon turnover and storage in soils where changes in soil microbial community structure and stimulation of the activity of microorganisms which prefer to grow on rhizodeposits may lead to a decrease in the composition of organic matter and result in an accumulation of soil carbon.

Impact of carbon and flooding on the metabolic diversity of microbial communities in soils

The assumption that carbon and soil water content are major determinants of microbial community structure and function is rarely questioned because of substantial evidence of the impacts of these variables on specific populations and functions. The significance of carbon and water for metabolic diversity at the microbial community level was tested on the field scale in agricultural plots varying in carbon inputs and in whether they were flooded. Surface soils in which rice straw was incorporated or burned and which were flooded or unflooded were sampled at monthly intervals three times during the flooded winter period (January to March) and again 1 month postdraining. Biomass carbon and nitrogen were not affected by treatments, active bacterial counts showed slight increases, and respiration rates were increased by carbon inputs and flooding. Biolog microplates were inoculated with soil extracts to quantify the metabolic diversity of the soil microbial community. Canonical correspondence analysis and the Monte Carlo permutation testing showed that differences in substrate utilization patterns were significantly related (P < 0.001) to carbon and flooding treatments. Biolog substrates whose metabolism was altered by the treatments were consistent across dates and tended to be positively related (utilization enhancement) to carbon inputs and negatively related to winter flooding. The importance of carbon as an environmental variable increased over time after straw treatment, whereas the importance of water became evident after flooding and decreased after drainage. The effect of long-term rice straw incorporation on substrate utilization patterns at another field site was consistent with these results despite the dissimilarities of the two soils.