Diversity of fungi, bacteria, and actinomycetes on leaves decomposing in a stream

Although fungi, bacteria, and specific bacterial taxa, such as the actinomycetes, have been studied extensively in various habitats, few studies have examined them simultaneously, especially on decomposing leaves in streams. In this study, sugar maple and white oak leaves were incubated in a stream in northeastern Ohio for 181 days during which samples were collected at regular intervals. Following DNA extraction, PCR-denaturing gradient gel electrophoresis (DGGE) was performed using fungus-, bacterium-, and actinomycete-specific primers. In addition, fungal and bacterial biomass was estimated. Fungal biomass differed on different days but not between leaves of the two species and was always greater than bacterial biomass. There were significant differences in bacterial biomass through time and between leaf types on some days. Generally, on the basis of DGGE, few differences in community structure were found for different leaf types. However, the ribotype richness of fungi was significantly greater than those of the bacteria and actinomycetes, which were similar to each other. Ribotype richness decreased toward the end of the study for each group except bacteria. Lack of differences between the two leaf types suggests that the microorganisms colonizing the leaf biofilm were primarily generalists that could exploit the resources of the leaves of either species equally well. Thus, we conclude that factors, such as the ecological role of the taxa (generalists versus specialists), stage of decay, and time of exposure, appeared to be more important determinants of microbial community structure than leaf quality.     

Assessing the Effect of Litter Species on the Dynamic of Bacterial and Fungal Communities during Leaf Decomposition in Microcosm by Molecular Techniques

Although bacteria and fungi are well-known to be decomposers of leaf litter, few studies have examined their compositions and diversities during the decomposition process in tropical stream water. Xishuangbanna is a tropical region preserving one of the highest floristic diversity areas in China. In this study, leaf litter of four dominant plant species in Xishuangbanna was incubated in stream water for 42 days during which samples were taken regularly. Following DNA extraction, PCR-DGGE (denaturing gradient gel electrophoresis) and clone-sequencing analyses were performed using bacterial and fungal specific primers. Leaf species have slightly influences on bacterial community rather than fungal community. The richness and diversity of bacteria was higher than that of fungi, which increased towards the end of the 42-day-incubation. The bacterial community was initially more specific upon the type of leaves and gradually became similar at the later stage of decomposition with alpha-proteobacteria as major component. Sequences affiliated to methanotrophs were obtained that indicates potentially occurrence of methane oxidation and methanogenesis. For the fungal community, sequences affiliated to Aspergillus were predominant at the beginning and then shifted to Pleosporales. Our results suggest that the microorganisms colonizing leaf biofilm in tropical stream water were mostly generalists that could exploit the resources of leaves of various species equally well.     

The rhizosphere microflora of wheat grown under controlled conditions I. The effect of soil fertility and urea leaf treatment on the rhizoplane microflora

Summary Microbial colonization of seminal roots of seedlings and of nodal roots of tillering plants was studied on spring wheat ‘Kaspar’ cultivated in growth, chambers. Methods were developed to microbially condition the soil before seeding and to regulate soil humidity. Addition of inorganic nutrients (NPK) to the soil increased the number of rhizoplane bacteria and actinomycetes, but did not effect the number of fungi on seminal and nodal roots. Urea leaf treatments stimulated bacteria and actinomycetes 7 and 9 days after treatment. Fourteen days after urea leaf treatment, however, bacterial numbers were mostly reduced, especially on seminal roots, while numbers of actinomycetes generally equalled the control. Root types and soil fertility did not obviously interact with the effect of urea leaf treatment on rhizoplane bacteria and actinomycetes. The only effect of urea on total numbers of fungi, was a reduction of their numbers on seminal roots 9 days after treatment at both NPK-levels.     

A culture-independent study of free-living fungi in biological soil crusts of the Colorado Plateau: their diversity and relative contribution to microbial biomass

Molecular methodologies were used to investigate free-living fungal communities associated with biological soil crusts (BSCs), along km-scale transects on the Colorado Plateau (USA). Two cyanobacteria-dominated crust types that did not contain significant lichen cover were examined. Fungal community diversity and composition were assessed with PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting and sequencing, and fungi-specific quantitative PCR was used to measure fungal population densities as compared with those of bacteria. Our results clearly indicate that free-living fungi, while ubiquitous in BSCs, are less diverse and contribute far less biomass than their bacterial counterparts. Biological soil crust fungal community structure differed from that of uncrusted soils in their surroundings. Phylogenetic analyses placed the majority of BSC fungi within the Ascomycota , confirmed the importance of dematiaceous fungi, and pointed to members of the genera Alternaria and Acremonium as the most common free-living fungi in these crusts. Phylotypes potentially representing novel taxa were recovered, as were several belonging to the Basidiomycota that would not have been readily recognized by culture-dependant means.     

Impact of agricultural practices on the Zea mays L. endophytic community

Agricultural practices are known to alter bulk soil microbial communities, but little is known about the effect of such practices on the plant endophytic community. We assessed the influence of long-term applications (20 years) of herbicides and different fertilizer types on the endophytic community of maize plants grown in different field experiments. Nested PCR-denaturing gradient gel electrophoresis (DGGE) analyses targeting general bacteria, type I or II methanotrophs, actinomycetes, and general fungi were used to fingerprint the endophytic community in the roots of Zea mays L. Low intraplant variability (reproducible DGGE patterns) was observed for the bacterial, type I methanotroph, and fungal communities, whereas the patterns for endophytic actinomycetes exhibited high intraplant variability. No endophytic amplification product was obtained for type II methanotrophs. Cluster and stability analysis of the endophytic type I methanotroph patterns differentiated maize plants cultivated by using mineral fertilizer from plants cultivated by using organic fertilizer with a 100% success rate. In addition, lower methanotroph richness was observed for mineral-fertilized plants than for organically fertilized plants. The use of herbicides could not be traced by fingerprinting the endophytic type I methanotrophs or by evaluating any other endophytic microbial group. Our results indicate that the effect of agrochemicals is not limited to the bulk microbial community but also includes the root endophytic community. It is not clear if this effect is due to a direct effect on the root endophytic community or is due to changes in the bulk community, which are then reflected in the root endophytic community.     

Leaf litter decomposition and microbial activity in nutrient-enriched and unaltered reaches of a headwater stream

SUMMARY 1. Decomposition of red maple ( Acer rubrum ) and rhododendron ( Rhododendron maximum ) leaves and activity of associated microorganisms were compared in two reaches of a headwater stream in Coweeta Hydrologic Laboratory, NC, U.S.A. The downstream reach was enriched with ammonium, nitrate, and phosphate whereas the upstream reach was not altered.
2. Decomposition rate, microbial respiration, fungal and bacterial biomass, and the sporulation rate of aquatic hyphomycetes associated with decomposing leaf material were significantly higher for both leaf types in the nutrient-enriched reach. Species richness and community structure of aquatic hyphomycetes also exhibited considerable changes with an increase in the number of fungal codominants in the nutrient-enriched reach.
3. Fungal biomass was one to two orders of magnitude greater than bacterial biomass in both reaches. Changes in microbial respiration rate corresponded to those in fungal biomass and sporulation, suggesting a primary role of fungi in leaf decomposition.
4. Nutrient enrichment increased microbial activity, the proportion of leaf carbon channelled through the microbial compartment and the decomposition rate of leaf litter.     

Rhizosphere soil microorganism populations and community structures of different watermelon cultivars with differing resistance to Fusarium oxysporum f. sp. niveum

Fusarium wilt is an increasingly serious disease of watermelon that reduces crop productivity. Changes in microorganism populations and bacterial and fungal community structures in rhizosphere soil of watermelon cultivars resistant or susceptible to Fusarium oxysporum f. sp. niveum were investigated using a plate culture method and PCR-DGGE analysis. Plate culture showed that populations of culturable bacteria and actinomycetes were more abundant in the rhizosphere of the resistant watermelon cultivar than the susceptible cultivar, but the fungi population had the opposite pattern. Populations of Penicillium , Fusarium , and Aspergillus were significantly lower in the resistant cultivar than the susceptible cultivar at the fruiting and uprooting stages (p?< 0.05). Pattern matching analysis generated the dendrogram of the DGGE results indicating the relatedness of the different resistant watermelon cultivars and their corresponding rhizosphere microbial communities. Further sequencing analysis of specific bands from DGGE profiles indicated that different groups of bacteria and fungi occurred in the rhizosphere of different watermelon cultivars. Our results demonstrated that plant genotype had a significant impact on soil microbial community structure, and the differences in the rhizosphere microbial community may contribute to the differences in resistance to F. oxysporum f. sp. niveum.     

Impact of Agricultural Practices on the Zea mays L. Endophytic Community

Agricultural practices are known to alter bulk soil microbial communities, but little is known about the effect of such practices on the plant endophytic community. We assessed the influence of long-term applications (20 years) of herbicides and different fertilizer types on the endophytic community of maize plants grown in different field experiments. Nested PCR-denaturing gradient gel electrophoresis (DGGE) analyses targeting general bacteria, type I or II methanotrophs, actinomycetes, and general fungi were used to fingerprint the endophytic community in the roots of Zea mays L. Low intraplant variability (reproducible DGGE patterns) was observed for the bacterial, type I methanotroph, and fungal communities, whereas the patterns for endophytic actinomycetes exhibited high intraplant variability. No endophytic amplification product was obtained for type II methanotrophs. Cluster and stability analysis of the endophytic type I methanotroph patterns differentiated maize plants cultivated by using mineral fertilizer from plants cultivated by using organic fertilizer with a 100% success rate. In addition, lower methanotroph richness was observed for mineral-fertilized plants than for organically fertilized plants. The use of herbicides could not be traced by fingerprinting the endophytic type I methanotrophs or by evaluating any other endophytic microbial group. Our results indicate that the effect of agrochemicals is not limited to the bulk microbial community but also includes the root endophytic community. It is not clear if this effect is due to a direct effect on the root endophytic community or is due to changes in the bulk community, which are then reflected in the root endophytic community.     

Summer season and long-term drought increase the richness of bacteria and fungi in the foliar phyllosphere of Quercus ilex in a mixed Mediterranean forest

We explored the changes in richness, diversity and evenness of epiphytic (on the leaf surface) and endophytic (within leaf tissues) bacteria and fungi in the foliar phyllosphere of Quercus ilex, the dominant tree species of Mediterranean forests. Bacteria and fungi were assessed during ontogenic development of the leaves, from the wet spring to the dry summer season in control plots and in plots subjected to drought conditions mimicking those projected for future decades. Our aim was to monitor succession in microbiota during the colonisation of plant leaves and its response to climate change. Ontogeny and seasonality exerted a strong influence on richness and diversity of the microbial phyllosphere community, which decreased in summer in the whole leaf and increased in summer in the epiphytic phyllosphere. Drought precluded the decrease in whole leaf phyllosphere diversity and increased the rise in the epiphytic phyllosphere. Both whole leaf bacterial and fungal richness decreased with the decrease in physiological activity and productivity of the summer season in control trees. As expected, the richness of epiphytic bacteria and fungi increased in summer after increasing time of colonisation. Under summer dry conditions, there was a positive relationship between TRF (terminal restriction fragments) richness and drought, both for whole leaf and epiphytic phyllosphere, and especially for fungal communities. These results demonstrate that changes in climate are likely to significantly alter microbial abundance and composition of the phyllosphere. Given the diverse functions and large number of phyllospheric microbes, the potential functional implications of such community shifts warrant exploration.     

Application of Fungal and Bacterial Production Methodologies to Decomposing Leaves in Streams

As leaves enter woodland streams, they are colonized by both fungi and bacteria. To determine the contribution of each of these microbial groups to the decomposition process, comparisons of fungal and bacterial production are needed. Recently, a new method for estimating fungal production based on rates of [(sup14)C]acetate incorporation into ergosterol was described. Bacterial production in environmental samples has been determined from rates of [(sup3)H]leucine incorporation into protein. In this study, we evaluated conditions necessary to use these methods for estimating fungal and bacterial production associated with leaves decomposing in a stream. During incubation of leaf disks with radiolabeled substrates, aeration increased rates of fungal incorporation but decreased bacterial production. Incorporation of both radiolabeled substrates by microorganisms associated with leaf litter was linear over the time periods examined (2 h for bacteria and 4 h for fungi). Incorporation of radiolabeled substrates present at different concentrations indicated that 400 nM leucine and 5 mM acetate maximized uptake for bacteria and fungi, respectively. Growth rates and rates of acetate incorporation into ergosterol followed similar patterns when fungi were grown on leaf disks in the laboratory. Three species of stream fungi exhibited similar ratios of rates of biomass increase to rates of acetate incorporation into ergosterol, with a mean of 19.3 (mu)g of biomass per nmol of acetate incorporated. Both bacterial and fungal production increased exponentially with increasing temperature. In the stream that we examined, fungal carbon production was 11 to 26 times greater than bacterial carbon production on leaves colonized for 21 days.     

Effects of Zn,Fe and Mn on Leaf Litter Breakdown by Aquatic Fungi: a Microcosm Study

We investigated the effects of heavy metals on leaf litter decomposition in streams. Leaves were immersed (10 days) at a reference (R) and a metal‐impacted (I) site and exposed in microcosms with increased Zn, Mn or Fe content, and to stream water from site R or I. Fungal biomass was higher in microcosms with leaves colonized at I and water from R. Fungal sporulation was higher in microcosms with leaves and water from R. Concentrations of 4.9, 9.6 and 5 ppm of Zn, Mn and Fe decrease fungal sporulation. The number of fungal species (spore counts and DGGE fingerprints) was lower in leaves colonized at site I. Cluster analyses of DGGE showed that Fe was the metal that most altered the structure of fungal community. Our results suggest that metal pollution affect leaf‐associated fungi depending on metal identity and concentration, and effects appear to be less pronounced in metal‐adapted communities. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

施肥和土壤管理对土壤微生物生物量碳、氮和群落结构的影响

以中国科学院沈阳生态试验站的长期定位试验为平台,研究了不同施肥和土壤管理对潮棕壤微生物生物量碳、氮和群落结构的影响。结果表明,裸地和农田处理的微生物生物量碳、氮较低,但是农田处理下施肥增加了微生物生物量,其中NPK+M效果最明显。DGGE图谱显示,处理间细菌条带分布较相似,其中裸地的细菌多样性最高;长期施肥和土壤管理改变了土壤真菌群落结构,施肥增加了真菌多样性,且有机肥的影响大于化肥;不同处理间氨氧化细菌群落结构差异显著,NPK+M显著增加了氨氧化细菌多样性,且无机肥和有机肥对氨氧化细菌群落影响不同。施肥和土壤管理对细菌影响较小,但显著改变了真菌和氨氧化细菌的群落结构。聚类分析结果显示,土壤管理措施较施肥对细菌、真菌和氨氧化细菌群落的影响更为显著。     

Macroinvertebrate community patterns in relation to leaf-associated periphyton under contrasting light and nutrient conditions in headwater streams

1. Temperate headwater streams traditionally have been considered heterotrophic and brown food web dominated with little primary production. Recent work, however, suggests algae on leaves in these streams may play a greater role than previously thought through interactions with microbial decomposers like fungi. Algae also may be important for macroinvertebrates colonizing leaves in streams. Algae are a more nutritious food resource for shredders than fungi and bacteria and provide a food resource for non-shredder macroinvertebrates.
2. In a field experiment, we manipulated light in three low-nutrient and three high-nutrient streams using leaf bags filled with red maple leaves in winter and spring. After four weeks we measured algal and fungal biomass, leaf stoichiometry, and macroinvertebrate abundance and biomass associated with the leaf bags. We also identified the macroinvertebrate community and examined differences in functional feeding guilds and taxa under ambient- and shaded-light treatments and low- and high-nutrient concentrations in relation to measured leaf characteristics.
3. Algal biomass on leaves was greatest in high-nutrient streams and ambient-light treatments in both seasons. Fungal biomass on leaves was greatest in high-nutrient streams and showed a moderate marginally significant positive correlation with algae during the winter. Leaf C:N was negatively correlated to algae in winter and fungi in both seasons, while leaf N:P and C:P were negatively correlated to fungi in winter and algae in spring. Interactions between fungi and algae on leaves and the nutritional importance of each for macroinvertebrates likely change across seasons, potentially impacting macroinvertebrate community composition.
4. Macroinvertebrate diversity did not differ, but biomass was significantly greater in shaded-light treatments during spring. Abundance was highest in the high-nutrient ambient-light conditions in both seasons, corresponding to greatest algal biomass. Functional feeding guild biomass and abundance were related to different leaf characteristics by season and guild. Higher algal biomass was an important factor for colonization of certain macroinvertebrates (e.g., Ephemerella (Ephemeroptera: Ephemerellidae) and Stenonema (Ephemeroptera: Heptageniidae)), while others were more abundant under shaded treatments with lower algal biomass (e.g., Tipula (Diptera: Tipulidae)), indicating taxa-specific responses.
5. Leaf-associated algae may be an important factor mediating macroinvertebrate communities associated with leaves in temperate headwater streams. Our results demonstrate that green and brown food webs intersect within leaf packs, and they cannot be easily disentangled. We therefore should consider both autochthonous and allochthonous resources within headwater streams when examining their communities or developing water management strategies.

     

Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time

The phyllosphere is colonized by a wide variety of bacteria and fungi; it harbors epiphytes, as well as plant-pathogenic bacteria and even human pathogens. However, little is known about how the bacterial community composition on leafy greens develops over time. The bacterial community of the leafy-green phyllosphere obtained from two plantings of rocket salad (Diplotaxis tenuifolia) and three plantings of lettuce (Lactuca sativa) at two farms in Norway were profiled by an Illumina MiSeq-based approach. We found that the bacterial richness of the L. sativa samples was significantly greater shortly (3 weeks) after planting than at harvest (5 to 7 weeks after planting) for plantings 1 and 3 at both farms. For the second planting, the bacterial diversity remained consistent at the two sites. This suggests that the effect on bacterial colonization of leaves, at least in part must, be seasonally driven rather than driven solely by leaf maturity. The distribution of phyllosphere communities varied between D. tenuifolia and L. sativa at harvest. The variability between these species at the same location suggests that the leaf-dwelling bacteria are not only passive inhabitants but interact with the host, which shapes niches favoring the growth of particular taxa. This work contributes to our understanding of host plant-specific microbial community structures and shows how these communities change throughout plant development.     

Species sorting and neutral processes are both important during the initial assembly of bacterial communities

Many studies have shown that species sorting, that is, the selection by local environmental conditions is important for the composition and assembly of bacterial communities. On the other hand, there are other studies that could show that bacterial communities are neutrally assembled. In this study, we implemented a microcosm experiment with the aim to determine, at the same time, the importance of species sorting and neutral processes for bacterial community assembly during the colonisation of new, that is, sterile, habitats, by atmospheric bacteria. For this we used outdoor microcosms, which contained sterile medium from three different rock pools representing different environmental conditions, which were seeded by rainwater bacteria. We found some evidence for neutral assembly processes, as almost every 4th taxon growing in the microcosms was also detectable in the rainwater sample irrespective of the medium. Most of these taxa belonged to widespread families with opportunistic growth strategies, such as the Pseudomonadaceae and Comamonadaceae, indicating that neutrally assembled taxa may primarily be generalists. On the other hand, we also found evidence for species sorting, as one out of three media selected a differently composed bacterial community. Species sorting effects were relatively weak and established themselves via differences in relative abundance of generalists among the different media, as well as media-specific occurrences of a few specific taxa. In summary, our results suggest that neutral and species sorting processes interact during the assembly of bacterial communities and that their importance may differ depending on how many generalists and specialists are present in a community.     

A Cross-System Comparison of Bacterial and Fungal Biomass in Detritus Pools of Headwater Streams

The absolute amount of microbial biomass and relative contribution of fungi and bacteria are expected to vary among types of organic matter (OM) within a stream and will vary among streams because of differences in organic matter quality and quantity. Common types of benthic detritus [leaves, small wood, and fine benthic organic matter (FBOM)] were sampled in 9 small (1st-3rd order) streams selected to represent a range of important controlling factors such as surrounding vegetation, detritus standing stocks, and water chemistry. Direct counts of bacteria and measurements of ergosterol (a fungal sterol) were used to describe variation in bacterial and fungal biomass. There were significant differences in bacterial abundance among types of organic matter with higher densities per unit mass of organic matter on fine particles relative to either leaves or wood surfaces. In contrast, ergosterol concentrations were significantly greater on leaves and wood, confirming the predominance of fungal biomass in these larger size classes. In general, bacterial abundance per unit organic matter was less variable than fungal biomass, suggesting bacteria will be a more predictable component of stream microbial communities. For 7 of the 9 streams, the standing stock of fine benthic organic matter was large enough that habitat-weighted reach-scale bacterial biomass was equal to or greater than fungal biomass. The quantities of leaves and small wood varied among streams such that the relative contribution of reach-scale fungal biomass ranged from 10% to as much as 90% of microbial biomass. Ergosterol concentrations were positively associated with substrate C:N ratio while bacterial abundance was negatively correlated with C:N. Both these relationships are confounded by particle size, i.e., leaves and wood had higher C:N than fine benthic organic matter. There was a weak positive relationship between bacterial abundance and streamwater soluble reactive phosphorus concentration, but no apparent pattern between either bacteria or fungi and streamwater dissolved inorganic nitrogen. The variation in microbial biomass per unit organic matter and the relative abundance of different types of organic matter contributed equally to driving differences in total microbial biomass at the reach scale.     

Distinct spatiotemporal succession of bacterial generalists and specialists in the lacustrine plastisphere

The assembly processes of generalists and specialists and their driving mechanisms during spatiotemporal succession is a central issue in microbial ecology but a poorly researched subject in the plastisphere. We investigated the composition variation, spatiotemporal succession, and assembly processes of bacterial generalists and specialists in the plastisphere, including non-biodegradable (NBMPs) and biodegradable microplastics (BMPs). Although the composition of generalists and specialists on NBMPs differed from that of BMPs, colonization time mainly mediated the composition variation. The relative abundance of generalists and the relative contribution of species replacement were initially increased and then decreased with colonization time, while the specialists initially decreased and then increased. Besides, the richness differences also affected the composition variation of generalists and specialists in the plastisphere, and the generalists were more susceptible to richness differences than corresponding specialists. Furthermore, the assembly of generalists in the plastisphere was dominated by deterministic processes, while stochastic processes dominated the assembly of specialists. The network stability test showed that the community stability of generalists on NBMPs and BMPs was lower than corresponding specialists. Our results suggested that different ecological assembly processes shaped the spatiotemporal succession of bacterial generalists and specialists in the plastisphere, but were less influenced by polymer types.     

Microbial Biomass,Respiration, and Decomposition of Hura crepitans L. (Euphorbiaceae) Leaves in a Tropical Stream1

The processing of leaves in temperate streams has been the subject of numerous studies but equivalent tropical ecosystems have received little attention. We investigated leaf breakdown of a tropical tree species (Hura crepitans, Euphorbiaceae), in a tropical stream using leaf bags (0.5 mm mesh) over a period of 24 days. We followed the loss of mass and the changes in adenosine triphosphate (ATP) concentrations and respiration rates associated with the decomposing leaves. The breakdown rate was fast (k=?0.0672/d, k_d=?0.0031/degree‐day), with 81 percent loss of the initial mass within 24 days. This high rate was probably related to the stable and high water temperature (22°C) favoring strong biological activity. Respiration rates increased until day 16 (1.1 mg O₂/h/g AFDM), but maximum ATP concentrations were attained at day 9 (725 nmol ATP/g AFDM) when leaf mass remaining was 52 percent. To determine the relative importance of fungi and bacteria during leaf decomposition, ATP concentrations, and respiration rates were determined in samples treated with antibiotics, after incubation in the stream. The results of the samples treated with the antifungal or the bacterial antibiotic suggest a higher contribution of the fungal community for total microbial biomass and a higher contribution of the bacterial community for microbial respiration rates, especially during the later stages of leaf decomposition. However, these results should be analyzed with caution since both antibacterial and antifungal agents did not totally eliminate microbial activity and biomass.     

Plant species richness,identity and productivity differentially influence key groups of microbes in grassland soils of contrasting fertility

The abundance of microbes in soil is thought to be strongly influenced by plant productivity rather than by plant species richness per se. However, whether this holds true for different microbial groups and under different soil conditions is unresolved. We tested how plant species richness, identity and biomass influence the abundances of arbuscular mycorrhizal fungi (AMF), saprophytic bacteria and fungi, and actinomycetes, in model plant communities in soil of low and high fertility using phospholipid fatty acid analysis. Abundances of saprophytic fungi and bacteria were driven by larger plant biomass in high diversity treatments. In contrast, increased AMF abundance with larger plant species richness was not explained by plant biomass, but responded to plant species identity and was stimulated by Anthoxantum odoratum. Our results indicate that the abundance of saprophytic soil microbes is influenced more by resource quantity, as driven by plant production, while AMF respond more strongly to resource composition, driven by variation in plant species richness and identity. This suggests that AMF abundance in soil is more sensitive to changes in plant species diversity per se and plant species composition than are abundances of saprophytic microbes.     

Bacterial Community Succession in Natural River Biofilm Assemblages

Temporal bacterial community changes in river biofilms were studied using 16S rRNA gene-based polymerase chain reaction–denaturing gradient gel electrophoresis (DGGE) followed by sequence analysis. Naturally occurring biofilms were sampled in 2001 during an undisturbed 7-month low-water period in the River Garonne (SW France). During the sampling period epilithic biomass exhibited a particular pattern: two 3-month periods of accumulation that resulted in two peaks in summer and fall, each at about 25 g ash-free dry mass per square meter. Bacterial community DGGE profiles differed between the summer and fall biomass peaks and shared only 30% common operational taxonomic units (OTUs), suggesting the influence of seasonal factors on these communities. During the second biomass accrual phase, bacterial richness and the appearance of new OTUs fitted a conceptual model of bacterial biofilm succession. During succession, five OTUs (corresponding to Dechloromonas sp., Nitrospira sp., and three different Spirosoma spp.) exhibited particular patterns and were present only during clearly defined successional stages, suggesting differences in life-history strategies for epilithic bacteria. Co-inertia analysis of DGGE banding patterns and physical–chemical data showed a significant relationship between community structure and environmental conditions suggesting that bacterial communities were mainly influenced by seasonal changes (temperature, light) and hydrodynamic stability. Within the periods of stability, analysis of environmental variables and community patterns showed the dominant influence of time and maturation on bacterial community structure. Thus, succession in these naturally occurring epilithic biofilm assemblages appears to occur through a combination of allogenic (seasonal) and autogenic changes.