Impact of <Emphasis Type="Italic">Phanerochaete chrysosporium</Emphasis> inoculation on indigenous bacterial communities during agricultural waste composting

This research was conducted to distinguish between the separate effects of the Phanerochaete chrysosporium inoculation and sample property heterogeneity induced by different inoculation regimes on the indigenous bacterial communities during agricultural waste composting. P. chrysosporium was inoculated during different phases. The bacterial community abundance and structure were determined by quantitative PCR and denaturing gradient gel electrophoresis analysis, respectively. Results indicated a significant stimulatory effect of P. chrysosporium inoculation on the bacterial community abundance. The bacterial community abundance significantly coincided with pile temperature, ammonium, and nitrate (P?<?0.006). Variance partition analysis showed that the P. chrysosporium inoculation directly explained 20.5 % (P?=?0.048) of the variation in the bacterial communities, whereas the sample property changes induced by different inoculation regimes indirectly explained up to 35.1 % (P?=?0.002). The bacterial community structure was significantly related to pile temperature, water-soluble carbon (WSC), and C/N ratio when P. chrysosporium were inoculated. The C/N ratio solely explained 7.9 % (P?=?0.03) of the variation in community structure, whereas pile temperature and WSC explained 7.7 % (P?=?0.026) and 7.5 % (P?=?0.034) of the variation, respectively. P. chrysosporium inoculation affected the indigenous bacterial communities most probably indirectly through increasing pile temperature, enhancing the substrate utilizability, and changing other physico-chemical factors.     

Determining the influence of environmental and patient specific factors on the polymicrobial communities of the cystic fibrosis airway

The aim of this study was to investigate the polymicrobial communities in an adult Cystic Fibrosis population stratified by gender and the most common CFTR mutation, F508del. In this pilot study, DNA was extracted from sputum samples of 29 adult patients (16 male: 13 female) with an F508del mutation in a stable clinical state. Universal primers were used to amplify DNA from bacterial and fungal communities and the resulting fragments were analysed by denaturing gradient gel electrophoresis. Bacterial profiles showed a significant effect of gender (P = 0.046) and P. aeruginosa carriage (P = 0.034) on community structure. Bacterial communities were found to be randomly assembled. Fungal community analysis found that F508del homozygous patients had a greater diversity than heterozygous patients (P = 0.007). This study indicates that the bacterial lung communities of adult CF patients are randomly assembled but have distinct gender based differences. Furthermore, the fungal communities colonising the CF lung are more diverse in F508 homozygotes. This is the first paper to identify a reduced bacterial diversity in female patients with CF and to implicate more severe CFTR genotypes with increased risk of infection with multiple fungal species.     

Factors Affecting Distribution of Earthworms in Kashmir Valley: A Multivariate Statistical Approach

Soil characteristics influence earthworm population dynamics, species distribution and community structure. According in the present study an attempt was made to determine the soil physiochemical factors influencing earthworms of Kashmir valley with a view to improve the soil productivity by enhancing earthworm diversity under different pedoecosystems. Data collection on 15 soil parameters from 20 earthworm inhabiting sites revealed significant variation within and among the sites in soil temperature (F_{23, 19} = 148.83, 9.71; P < 0.05), moisture (F_{23, 19} = 16.91, 46.20; P < 0.05), pH (F₁₉ = 47.21; P < 0.05), electrical conductivity (F_{23, 19} = 11.67, 87.13; P < 0.05), sodium (F_{23, 19} = 2.46, 211.25; P < 0.05), potassium (F₁₉ = 22.91; P < 0.05), calcium (F₁₉ = 15.90; P < 0.05), magnesium (F_{23, 19} = 1.76, 104.51; P < 0.05), organic carbon (F_{23, 19} = 64.60, 222.50; P < 0.05), organic nitrogen (F_{23, 19} = 4.59, 3.81; P < 0.05) and phosphorous (F_{23, 19} = 5.11, 137.87; P < 0.05). Aporrectodea caliginosa trapezoides and A. rosea rosea exhibited wide range of distribution whereas Octolasion cyaneum, A. c. trapezoides and A. parva showed restricted distribution. Hierarchical cluster analysis grouped 20 earthworm collection sites into three clusters—earthworm absent sites, low earthworm diversity sites and moderate earthworm diversity sites. Principal component analysis assisted from the data set of 20 sites, resulting into four latent factors accounting for 77.95 % of total variance, identified the factors affecting earthworm communities are mainly related to physical habitat factor, chemical factor, soil texture factor and growth factor, each accounting for 26.41, 20.16, 18.25 and 13.13 % of total variance respectively.     

Changes in Bacterial and Fungal Communities across Compost Recipes,Preparation Methods,and Composting Times

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.     

The influence of goethite and gibbsite on soluble nutrient dynamics and microbial community composition

Iron and aluminum (oxyhydr)oxides are ubiquitous in the soil environment and have the potential to strongly affect the properties of dissolved organic matter. We examined the effect of oxide surfaces on soluble nutrient dynamics and microbial community composition using an incubation of forest floor material in the presence of (1) goethite and quartz, (2) gibbsite and quartz, and (3) quartz surfaces. Forest floor material was incubated over a period of 154 days. Aqueous extracts of the incubations were harvested on days 5, 10, 20, 30, 60, 90, and 154, and concentrations of P, N, PO₄ ^3?, NO₂ ^?, NO₃ ^?, and organic C were measured in the solutions. Microbial community composition was examined through pyrosequencing of bacterial and fungal small subunit ribosomal RNA genes on selected dates throughout the incubation. Results indicated that oxide surfaces exerted strong control on soluble nutrient dynamics and on the composition of the decomposer microbial community, while possibly having a small impact on system-level respiration. Goethite and gibbsite surfaces showed preferential adsorption of P-containing and high molar mass organic solutes, but not of N-containing compounds. On average, organic C concentrations were significantly lower in water extractable organic matter (WEOM) solutions from oxide treatments than from the control treatment (P = 0.0037). Microbial community composition varied both among treatments and with increasing time of incubation. Variation in bacterial and fungal community composition exhibited strong-to-moderate correlation with length of incubation, and several WEOM physiochemical characteristics including apparent (weight averaged) molar mass, pH and electrical conductivity. Additionally, variation in bacterial community composition among treatments was correlated with total P (r = 0.60, P < 0.0001), PO₄ ^3? (r = 0.79, P < 0.0001), and organic C (r = 0.36, P = 0.015) concentrations; while variation in fungal communities was correlated with organic C concentrations (r = ?0.48, P = 0.0008) but not with phosphorus concentrations. The relatively small impact of oxide surfaces on system-level microbial respiration of organic matter despite their significant effects on microbial community composition and WEOM dynamics lends additional support to the theory of microbial functional redundancy.     

Variation in microbial population during composting of agro-industrial waste

Two compost piles were prepared, using two ventilation systems: forced ventilation and ventilation through mechanical turning. The material to compost was a mixture of orange waste, olive pomace, and grass clippings (2:1:1 v/v). During the composting period (375 days), samples were periodically taken from both piles, and the enumeration of fungi, actinomycetes, and heterotrophic bacteria was carried out. All studied microorganisms were incubated at 25 and 55 °C after inoculation in appropriate growth media. Fungi were dominant in the early stages of both composting processes; heterotrophic bacteria proliferated mainly during the thermophilic stage, and actinomycetes were more abundant in the final stage of the composting process. Our results showed that the physical and chemical parameters: temperature, pH, moisture, and aeration influenced the variation of the microbial population along the composting process. This study demonstrated that composting of these types of wastes, despite the prolonged mesophilic stage, provided an expected microbial variation.     

Effect of root exudates on beneficial microorganisms—evidence from a continuous soybean monoculture

Soybean (Glycine max) agriculture is characterized by a high proportion of mono-cropping which results in reduced crop production in the Northeast China. Among all biotic and abiotic factors, changes in soil microbial communities induced by root activities, especially root exudates, might play an important role in these effects. The aim of the present study was to investigate response of microbial biomass and two major beneficial microbial functional groups, ammonia-oxidizing bacteria (AOB), and arbuscular mycorrhizal fungi (AMF), to root exudates in an experimental field under continuous soybean monoculture for 13 years. The results showed that microbial biomass carbon changed significantly with years of mono-cropping and correlated with concentrations of genistein (r = 0.4399, P < 0.001) and daidzein (r = 0.4082, P < 0.05) in the rhizosphere. However, root exudates had little effect on the nitrifier community, but reduced nitrification in the rhizosphere. In contrast, total AMF hyphal length was significantly stimulated by genistein (r = 0.5252, P < 0.01). There was a trend that AMF spore density increased in the rhizosphere with increasing years of mono-cropping, while AMF infection was constant over time, which might be attributed to competition between AMF and soil-borne fungal pathogens, as the results of stimulatory effect of flavonoids on fungal community, especially fungal pathogens. Our results suggested that the yield reduction in the beginning of continuous soybean monoculture could be partially attributed to nitrogen availability and yield stabilization after few years to stimulatory effects on AMF. These results imply that some of plant root exudates play a crucial role in changing the soil microbial community, and that underground ecosystem functioning is also affected by interactions among microbial functional groups.     

Shorebird assemblages respond to anthropogenic stress by altering habitat use in a wetland in India

Shorebirds are globally experiencing declines due to habitat loss and anthropogenic disturbance. The Central Asian Flyway hosts significant shorebirds that winter in the Indian subcontinent. The current study examined the shorebird assemblages of Kadalundi-Vallikkunnu Community Reserve, an internationally important estuarine wetland in southwestern India, to determine changes in their assemblages in relation to habitat alterations. We conducted point counts from 2005 to 2012 in mudflats, mangroves, sandy beaches and shallow water areas in Kadalundi-Vallikkunnu Community Reserve. This study measured physicochemical variables as a proxy for anthropogenic change experienced as a result of rapidly increasing human populations combined with development. We examined rainfall data during the study period to determine associations with shorebird abundance. Stepwise linear regression showed that total nitrogen and rainfall were significantly related to shorebird abundance (bird count = 306 + 213 NO₃ ^?—1.13 rainfall, F = 31.20, p < 0.001). High rainfall in a given year (one-way ANOVA F = 19.91, p < 0.001) and the previous year resulted in lower shorebird counts (one-way ANOVA F = 16.01, p < 0.001). Shorebirds declined during the study period and habitat use shifted significantly from mangroves and mudflats to sandy beaches (one-way ANOVA, F = 2.18, p = 0.034). Shorebirds also exhibited a gradual decline in diversity. We conclude that altered nutrient content in this wetland resulted in changes in the prey base in the four habitat types. Shorebirds responded to these changes by increasing the use of less preferred habitat (sandy beaches). The anthropogenic influences on the wetland are large (waste disposal, sand mining, disturbance due to development) and continued pressure may result in further decline of shorebird assemblages. The results from this study indicate that certain anthropogenic disturbances, such as waste disposal and sand mining, should be reduced to maintain and improve the integrity of this wetland.     

Effect of inoculating white-rot fungus during different phases on the compost maturity of agricultural wastes

The lignocellulolytic microorganism, Phanerochaete chrysosporium, was inoculated during different phases of agricultural wastes composting, and its effect on compost maturity was studied. In the three runs, the decrease in C/N ratio and increases in germination index and humification indices (humification ratio, humification index, percentage of humic acids and degree of polymerisation) were found. Furthermore, the different effects of inoculation during different phases on the compost maturity could be observed by using ANOVA. When inoculated during the second fermentation phase, P. chrysosporium induced significant changes on all parameters of compost maturity except C/N ratio, whereas it did not produce an obvious change on these parameters when inoculated during the first fermentation phase.     

Interactions between fungal growth,substrate utilization,and enzyme production during solid substrate cultivation of Phanerochaete chrysosporium on cotton stalks

Fungal pretreatment, using lignin-degrading microorganisms to improve lignocellulosic feedstocks with minimal energy input, is a potential alternative to physiochemical pretreatment methods. Identifying the kinetics for fungal pretreatment during solid substrate cultivation is needed to help establish the processing conditions for effective scale up of this technology. In this study, a set of mathematical models were proposed for describing the interactions between holocellulose consumption, lignin degradation, cellulase, ligninolytic enzyme, and the growth of Phanerochaete chrysosporium during a 14 day fungal pretreatment process. Model parameters were estimated and validated by the System Biology Toolbox in MatLab. Developed models provided sufficiently accurate predictions for fungal growth (R ² = 0.97), holocellulose consumption (R ² = 0.97), lignin degradation (R ² = 0.93) and ligninolytic enzyme production (R ² = 0.92), and fair prediction for cellulase production (R ² = 0.61). The models provide valuable information for understanding the interactive mechanisms in biological systems as well as for fungal pretreatment process scale up and improvement.     

Ectomycorrhizal fungal succession coincides with shifts in organic nitrogen availability and canopy closure in post-wildfire jack pine forests

Successional changes in belowground ectomycorrhizal fungal (EMF) communities have been observed with increasing forest stand age; however, mechanisms behind this change remain unclear. It has been hypothesized that declines of inorganic nitrogen (N) and increases of organic N influence changes in EMF taxa over forest development. In a post-wildfire chronosequence of six jack pine (Pinus banksiana) stands ranging in age from 5 to 56 years, we investigated EMF community composition and compared shifts in taxa with detailed soluble inorganic and organic N data. Taxa were identified by internal transcribed spacer rDNA sequencing, and changes in community composition evaluated with non-metric multi-dimensional scaling (NMDS). Dissimilarities in the community data were tested for correlations with N variables. We observed a successional shift along NMDS axis 1 from such taxa as Suillus brevipes and Thelephora terrestris in sites age 5 and 11 to species of Cortinarius and Russula, among others, in the four older sites. This change was positively correlated with soluble organic N (SON) (r ² = 0.902, P = 0.033) and free amino-acid N (r ² = 0.945, P = 0.021), but not inorganic N. Overall, our results show a successional shift of EMF communities occurring between stand initiation and canopy closure without a change in species of the dominant plant–host, and associated with SON and free amino-acid N in soil. It is uncertain whether EMF taxa are responding to these organic N forms directly, affecting their availability, or are ultimately responding to changes in other site variables, such as belowground productivity.     

Diversity and Functionality of Arbuscular Mycorrhizal Fungi in Three Plant Communities in Semiarid Grasslands National Park, Canada

Septate endophytes proliferating in the roots of grasslands’ plants shed doubts on the importance of arbuscular mycorrhizal (AM) symbioses in dry soils. The functionality and diversity of the AM symbioses formed in four replicates of three adjacent plant communities (agricultural, native, and restored) in Grasslands National Park, Canada were assessed in periods of moisture sufficiency and deficiency typical of early and late summer in the region. The community structure of AM fungi, as determined by polymerase chain reaction-denaturing gradient gel electrophoresis, varied with sampling time and plant community. Soil properties other than soil moisture did not change significantly with sampling time. The DNA sequences dominating AM extraradical networks in dry soil apparently belonged to rare taxa unreported in GenBank. DNA sequences of Glomus viscosum, Glomus mosseae, and Glomus hoi were dominant under conditions of moisture sufficiency. In total, nine different AM fungal sequences were found suggesting a role for the AM symbioses in semiarid areas. Significant positive linear relationships between plant P and N concentrations and active extraradical AM fungal biomass, estimated by the abundance of the phospholipid fatty acid marker 16:1ω5, existed under conditions of moisture sufficiency, but not under dry conditions. Active extraradical AM fungal biomass had significantly positive linear relationship with the abundance of two early season grasses, Agropyron cristatum (L.) Gaertn. and Koeleria gracilis Pers., but no relationship was found under dry conditions. The AM symbioses formed under conditions of moisture sufficiency typical of early summer at this location appear to be important for the nutrition of grassland plant communities, but no evidence of mutualism was found under the dry conditions of late summer.     

Nitrite reductase genes as functional markers to investigate diversity of denitrifying bacteria during agricultural waste composting

The purpose of this study was to investigate the diversity of denitrifier community during agricultural waste composting. The diversity and dynamics of the denitrifying genes (nirK and nirS) were determined using polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE). Relationships between physico-chemical parameters and denitrifying genes structures were simultaneously evaluated by redundancy analysis (RDA). Phylogenetic analysis indicated that nirK clones grouped into six clusters and nirS clones into two major clusters, respectively. The results showed a very high diversity of nir gene sequences within composting samples. RDA showed that the nirK and nirS gene structures were significantly related to pH and pile temperature (P?<?0.05). Significant amounts of the variation (49.2 and 38.3 % for nirK and nirS genes, respectively) were explained by pH and pile temperature, suggesting that those two parameters were the most likely ones to influence, or be influenced by the denitrifiers harboring nirK and nirS genes.     

Lespedeza cuneata invasion alters soils facilitating its own growth

Lespedeza cuneata (sericea) is an Asian legume introduced to the US in the 1930s for erosion control and forage, but it can strongly reduce the abundance of native grassland plants. One possible explanation for this high invasive capacity is that L. cuneata is able to alter soil conditions to either improve its own growth, or reduce growth of native plants. To test for soil alteration following invasion, we collected soil from a previous 3-year field experiment in which L. cuneata was established in or excluded from randomly selected plots in a restored grassland. These soil history treatments were crossed with soil autoclaving—to disrupt microbial communities potentially important to plant interactions. For each treatment combination, a native plant, Sorghastrum nutans, was grown with L. cuneata or a conspecific in a 12-week greenhouse experiment. Although we found no evidence for competitive effects on the native species, L. cuneata biomass increased when grown in soil with a L. cuneata history as opposed to non-invaded soil (F _{1, 16} = 4.79, P = 0.04). Additionally, nodulation of L. cuneata increased in invaded compared to non-invaded soil (F _{1, 16} = 6.01, P = 0.026). These results indicate that, within three years of invasion, L. cuneata is able to alter soils to facilitate its own growth and suggest that at least part of the invasive success of L. cuneata is linked to altered soil conditions.     

A comparison of culture-dependent and culture-independent techniques used to characterize bacterial communities on healthy and white plague-diseased corals of the Montastraea annularis species complex

Diseases of hermatypic corals pose a global threat to coral reefs, and investigations of bacterial communities associated with healthy corals and those exhibiting signs of disease are necessary for proper diagnosis. One disease, commonly called white plague (WP), is characterized by acute tissue loss. This investigation compared the bacterial communities associated with healthy coral tissue (N = 15), apparently healthy tissue on WP-diseased colonies (N = 15), and WP-diseased tissues (N = 15) from Montastraea annularis (species complex) colonies inhabiting a Bahamian reef. Aliquots of sediment (N = 15) and water (N = 15) were also obtained from the proximity of each coral colony sampled. Samples for culture-dependent analyses were inoculated onto one-half strength Marine Agar (½ MA) and Thiosulfate Citrate Bile Salts Sucrose Agar to quantify the culturable communities. Length heterogeneity PCR (LH-PCR) of the 16S rRNA gene characterized the bacterial operational taxonomic units (OTU) associated with lesions on corals exhibiting signs of a white plague-like disease as well as apparently healthy tissue from diseased and non-diseased conspecifics. Analysis of Similarity was conducted on the LH-PCR fingerprints, which indicated no significant difference in the composition of bacterial communities associated with apparently healthy and diseased corals. Comparisons of the 16S rRNA gene amplicons from cultured bacterial colonies (½ MA; N = 21) with all amplicons obtained from the whole coral-associated bacterial community indicated ≥39 % of coral-associated bacterial taxa could be cultured. Amplicons from these bacterial cultures matched amplicons from the whole coral-associated bacterial community that, when combined, accounted for >70 % total bacterial abundance. An OTU with the same amplicon length as Aurantimonas coralicida (313.1 bp), the reported etiological agent of WPII, was detected in relatively low abundance (<0.1 %) on all tissue types. These findings suggest a coral disease resembling WP may result from multiple etiologies.     

Soil fungal community variation by large-scale reclamation in Sanjiang plain,China

Large-scale marshland reclamation can cause substantial changes to the soil fungal community by disturbances associated with the growth of crop plants and by the addition of fertilizers and pesticides. In this study, high-throughput sequencing of the fungal-specific internal transcribed spacer (ITS) gene region was used to identify fungal taxa. We analyzed the variation in soil fungi diversity and community composition in marshland, paddy, and farmland corn soils, and investigated the relationship between soil fungal community composition and soil physicochemical characteristics to quantify the effect of large-scale reclamation on marshland soil environment in the Sanjiang Plain, northeast China. Marshland soil contained most of the 1997 operational taxonomic units (OTUs) found across all sites (1241), while paddy soil had only 614 OTUs and farmland corn soil 817 OTUs. All reclaimed lands presented a decline in richness and diversity of soil fungi at the OTU level, and soil fungal richness was significantly different between marshland and reclaimed sites (P < 0.05), although it did not differ significantly between marshland and farmland corn sites. Additionally, soil fungal community composition showed different trends and structure after the reclamation. One-way analysis of variance showed Basidiomycota, Zygomycota, Glomeromycota, and Chytridiomycota composition differed significantly between marshland and reclaimed sites (P < 0.05). Nine dominant genera (relative abundance >1.5% in at least one site) and many unclassified genera showed significant variation between marshland and reclaimed sites, including Blumeria, Tomentella, Peziza, Hypholoma, Zopfiella, Mrakia, and Fusarium. Soil fungal community composition and diversity were affected by soil moisture, pH, total carbon (C), available nitrogen (N), soil organic carbon, soil dissolved organic carbon, and C/N (the ratio of total carbon to total nitrogen). The present results contribute to understanding the fungal community in marshland ecosystems, and the role of environmental variability as a predictor of fungal community composition.     

High level of genetic variation within clonal orchid Goodyera repens

Type of reproduction has an important effect on the maintenance of particular populations and species persistence in time and space. This trait significantly influences the ecological and genetic structure of populations, and in consequence the evolution of species. The primary objectives of this study were: to estimate genetic diversity within and among populations of clonal species Goodyera repens from different populations in northeastern Poland, and to amount factors shaping the genetic structure of this orchid. Based on 451 rosettes of G. repens from 11 localities in northeastern Poland, we conducted a genetic population analysis using allozymes. We included information on population size, flowering, fruit set and seed dispersal to elucidate their influences on genetic diversity of this species. Populations differed according to demographic properties. The majority of seeds (86.4–94.8 %) were found at a distance of 0.2 m. We observed a high level of genetic (P _PL = 50 %, A = 1.68, H _O = 0.210, H _E = 0.204) and genotypic diversity (G = 163, G/N _S = 0.66, G _U = 30.2 %), and low but statistically significant genetic differentiation among populations (F _ST = 0.060; P < 0.001). We suggest that the genetic diversity of G. repens is mainly an effect of the abundance of pine and spruce forest communities suitable for this species in NE Poland and the high level of sexual reproduction.     

Little evidence for niche partitioning among ectomycorrhizal fungi on spruce seedlings planted in decayed wood versus mineral soil microsites

Ectomycorrhizal fungal (EMF) communities vary among microhabitats, supporting a dominant role for deterministic processes in EMF community assemblage. EMF communities also differ between forest and clearcut environments, responding to this disturbance in a directional manner over time by returning to the species composition of the original forest. Accordingly, we examined EMF community composition on roots of spruce seedlings planted in three different microhabitats in forest and clearcut plots: decayed wood, mineral soil adjacent to downed wood, or control mineral soil, to determine the effect of retained downed wood on EMF communities over the medium and long term. If downed and decayed wood provide refuge habitat distinct from that of mineral soil, we would expect EMF communities on seedlings in woody habitats in clearcuts to be similar to those on seedlings planted in the adjacent forest. As expected, we found EMF species richness to be higher in forests than clearcuts (P ≤ 0.01), even though soil nutrient status did not differ greatly between the two plot types (P ≥ 0.05). Communities on forest seedlings were dominated by Tylospora spp., whereas those in clearcuts were dominated by Amphinema byssoides and Thelephora terrestris. Surprisingly, while substrate conditions varied among microsites (P ≤ 0.03), especially between decayed wood and mineral soil, EMF communities were not distinctly different among microhabitats. Our data suggest that niche partitioning by substrate does not occur among EMF species on very young seedlings in high elevation spruce-fir forests. Further, dispersal limitations shape EMF community assembly in clearcuts in these forests.     

Bioaugmentation of a methyl parathion contaminated soil with Pseudomonas sp. strain WBC-3

Pseudomonas sp. strain WBC-3 utilizes methyl parathion (MP) and para-nitrophenol as the sole source of carbon, nitrogen and energy. In this study, strain WBC-3 was inoculated into lab-scale MP-contaminated soil for bioaugmentation. Accelerated removal of MP was achieved in bioaugmentation treatment compared to non-bioaugmentation treatment, with complete removal of 0.536 mg g⁻¹ dry soil in bioaugmentation treatment within 15 days and without accumulation of toxic intermediates. The analysis of denaturing gradient gel electrophoresis and real-time PCR showed that strain WBC-3 existed stably during the entire bioaugmentation period. Simultaneously, redundancy analysis for evaluating the relationships between the environmental factors and microbial community structure indicated that the indigenous bacterial community structure was significantly influenced by strain WBC-3 inoculation (P = 0.002).     

Biocontrol agent Fusarium oxysporum f.sp. strigae has no adverse effect on indigenous total fungal communities and specific AMF taxa in contrasting maize rhizospheres

We studied the effects of Fusarium oxysporum f.sp. strigae (Fos), a soil-borne biocontrol agent (BCA) against Striga hermonthica, on total fungal and arbuscular mycorrhizal fungal (AMF) taxa in rhizospheres of maize in both clayey and sandy soil. Effects of Fos-BCA ‘Foxy-2’ were evaluated against (1) S. hermonthica presence, and (2) organic fertilization with Tithonia diversifolia residues at 14, 28 and 42 d after ‘Foxy-2’ inoculation, via DNA-based quantitative PCR and TRFLP fingerprinting. In both soils, ‘Foxy-2’ occasionally promoted total fungal abundance, while the community composition was mainly altered by T. diversifolia and S. hermonthica. Notably, ‘Foxy-2’ stimulated AMF Gigaspora margarita abundance, while G. margarita was suppressed by S. hermonthica. Total fungal and AMF abundance were promoted by T. diversifolia residues. In conclusion, ‘Foxy-2’ resulted in no adverse effects on indigenous rhizosphere fungal communities substantiating its environmental safety as BCA against S. hermonthica.