Microbial succession in the rhizosphere of live and decomposing barley roots as affected by the antagonistic strain Pseudomonas fluorescens DR54-BN14 or the fungicide imazalil

Effects of tea oil camellia (Camellia oleifera Abel.) shell-based organic fertilizers on the physicochemical property and microbial community structure of the rhizosphere soil

Soil microorganisms play important roles in promoting soil ecosystem restoration, but much of the current research has been limited to changes in microbial community structure in general, and little is known regarding the soil physicochemical property and microbial community structure. In this study, four organic fertilizers were first prepared based on tea oil camellia shell (TOCS). Our findings indicate that the application of BOFvo increased both total pore volume and BET surface area of the rhizosphere soils, as well there was a remarkable enhancement in total organic matter (TOM), total nitrogen (TN), available nitrogen (AN), total phosphorus (TP), total potassium (TK), and available potassium (AK) contents of the rhizosphere soils. Meanwhile, in comparison to the CK and CF groups, the utilization of BOFvo led to a substantial increase in both average yield and fruiting rate per plant at maturity, as well resulted in a significant increase in TN and TP contents of tea oil camellia leaves. Furthermore, our findings suggest that the application of TOCS-based organic fertilizers significantly enhances the microbial diversity in the rhizosphere soils with Proteobacteria and Ascomycota being the dominant bacterial and fungal phyla, respectively, and Rhodanobacter and Fusarium being the dominant bacterial and fungal genus, respectively. Redundancy analysis (RDA) indicates that the physicochemical characteristics of TOCS-based organic fertilizers had a significant impact on the composition and distribution of microbial communities in the rhizosphere soils. This study will facilitate the promotion and application of TOCS-based organic fertilizers, thereby establishing a foundation for the reuse of tea oil camellia waste resources.

Effect of Re-acidification on Buffalo Grass Rhizosphere and Bulk Microbial Communities During Phytostabilization of Metalliferous Mine Tailings

Phytostabilized highly acidic, pyritic mine tailings are susceptible to re-acidification over time despite initial addition of neutralizing amendments. Studies examining plant-associated microbial dynamics during re-acidification of phytostabilized regions are sparse. To address this, we characterized the rhizosphere and bulk bacterial communities of buffalo grass used in the phytostabilization of metalliferous, pyritic mine tailings undergoing re-acidification at the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, AZ. Plant-associated substrates representing a broad pH range (2.35-7.76) were sampled to (1) compare the microbial diversity and community composition of rhizosphere and bulk compartments across a pH gradient, and (2) characterize how re-acidification affects the abundance and activity of the most abundant plant growth-promoting bacteria (PGPB; including N2-fixing) versus acid-generating bacteria (AGB; including Fe-cycling/S-oxidizing). Results indicated that a shift in microbial diversity and community composition occurred at around pH 4. At higher pH (>4) the species richness and community composition of the rhizosphere and bulk compartments were similar, and PGPB, such as Pseudomonas, Arthrobacter, Devosia, Phyllobacterium, Sinorhizobium, and Hyphomicrobium, were present and active in both compartments with minimal presence of AGB. In comparison, at lower pH (<4) the rhizosphere had a significantly higher number of species than the bulk (p < 0.05) and the compartments had significantly different community composition (unweighted UniFrac; PERMANOVA, p < 0.05). Whereas some PGPB persisted in the rhizosphere at lower pH, including Arthrobacter and Devosia, they were absent from the bulk. Meanwhile, AGB dominated in both compartments; the most abundant were the Fe-oxidizer Leptospirillum and Fe-reducers Acidibacter and Acidiphilium, and the most active was the Fe-reducer Aciditerrimonas. This predominance of AGB at lower pH, and even their minimal presence at higher pH, contributes to acidifying conditions and poses a significant threat to sustainable plant establishment. These findings have implications for phytostabilization field site management and suggest re-application of compost or an alternate buffering material may be required in regions susceptible to re-acidification to maintain a beneficial bacterial community conducive to long-term plant establishment.

Response of microbial communities from an apple orchard and grassland soils to the first-time application of the fungicide tetraconazole

The aim of the study was to assess the impact of the triazole fungicide tetraconazole applied at the field rate (FR) and at ten-fold the FR (10FR) on microorganisms in orchard soil with a long-term history of fungicides application and in grassland soil that had not previously been treated with pesticides. To ascertain this impact, the microbial activity determined by fluorescein diacetate (FDA) hydrolysis, the culturable number of bacteria, fungi and tetraconazole-resistant fungi, and the phospholipid microbial biomass and the structural and functional biodiversity assessed by the PLFA and Biolog approaches, respectively, were examined under laboratory conditions during 28-day experiment. The response of soil microorganisms to the fungicide tetraconazole, which had never been used before in these soils, depended on the management of the soils. In apple orchard soil that had been treated with FR or 10FR tetraconazole, a decrease in microbial activity was still observed on the 28th day after the application of the fungicide. In contrast, a significant impact of tetraconazole on the number of bacteria was still observed at the end of experiment in grassland soil. Results of principal component analysis (PCA) indicated that the application of tetraconazole significantly changed the structure of the microbial communities in the orchard soil. In addition, analysis of the Biolog profiles revealed a decrease in the catabolic activity of the microbial communities in grassland soil that had been treated with tetraconazole at both rates over time. The evaluation of the structural and functional diversity of microbial communities using PCA appears to be the most valuable monitoring tool for assessing the impact of tetraconazole application on soil microorganisms.

Importance of inoculum properties on the structure and growth of bacterial communities during Recolonisation of humus soil with different pH

The relationship between community structure and growth and pH tolerance of a soil bacterial community was studied after liming in a reciprocal inoculum study. An unlimed (UL) humus soil with a pH of 4.0 was fumigated with chloroform for 4 h, after which < 1 % of the initial bacterial activity remained. Half of the fumigated soil was experimentally limed (EL) to a pH of 7.6. Both the UL and the EL soil were then reciprocally inoculated with UL soil or field limed (FL) soil with a pH of 6.2. The FL soil was from a 15-year-old experiment. The structural changes were measured on both bacteria in soil and on bacteria able to grow on agar plates using phospholipids fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analysis. The developing community pH tolerance and bacterial growth were also monitored over time using thymidine incorporation. The inoculum source had a significant impact on both growth and pH tolerance of the bacterial community in the EL soil. These differences between the EL soil inoculated with UL soil and FL soil were correlated to structural changes, as evidenced by both PLFA and DGGE analyses on the soil. Similar correlations were seen to the fraction of the community growing on agar plates. There were, however, no differences between the soil bacterial communities in the unlimed soils with different inocula. This study showed the connection between the development of function (growth), community properties (pH tolerance) and the structure of the bacterial community. It also highlighted the importance of both the initial properties of the community and the selection pressure after environmental changes in shaping the resulting microbial community.

Microbial community in the rhizosphere of young maize seedlings is susceptible to the impact of introduced pseudomonads as indicated by FAME analysis

Two species of Pseudomonas (i.e. P. chlororaphis or P. putida) derived from a maize rhizosphere were studied for their impact on the structure of the microbial community in the rhizosphere of young maize seedlings after inoculation. The culturable bacteria and total microbial communities were analyzed based on profiles of whole-cell fatty acid methyl esters (MIDI-FAME). The introduction of Pseudomonas species resulted in the shift from the Gram-positive dominated culturable community in the rhizosphere of uninoculated maize to more Gram-negative populations in the rhizospheres of the inoculated plants. For the total rhizosphere communities, 43, 47 and 42 FAMEs were detected in the uninoculated maize and the samples inoculated with P. chlororaphis or P. putida, respectively. In contrast to the culturable communities, low concentrations of marker FAMEs for Gram-positives (i15:0, a15:0, i16:0) were found in the profiles of the total rhizosphere communities. The maize inoculations resulted in an enrichment of some Gram-negative isolates; however, Gram-positive bacteria, Cytophaga/Flavobacterium and saprophytic fungi were found in the uninoculated rhizosphere.

Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops

Seasonal shifts in rhizosphere microbial populations were investigated to follow the influence of plant developmental stage. A field study of indigenous microbial rhizosphere communities was undertaken on pea (Pisum satvium var. quincy), wheat (Triticum aestivum var. pena wawa) and sugar beet (Beta vulgaris var. amythyst). Rhizosphere community diversity and substrate utilization patterns were followed throughout a growing season, by culturing, rRNA gene density gradient gel electrophoresis and BIOLOG. Culturable bacterial and fungal rhizosphere community densities were stable in pea and wheat rhizospheres, with dynamic shifts observed in the sugar beet rhizosphere. Successional shifts in bacterial and fungal diversity as plants mature demonstrated that different plants select and define their own functional rhizosphere communities. Assessment of metabolic activity and resource utilization by bacterial community-level physiological profiling demonstrated greater similarities between different plant species rhizosphere communities at the same than at different developmental stages. Marked temporal shifts in diversity and relative activity were observed in rhizosphere bacterial communities with developmental stage for all plant species studied. Shifts in the diversity of fungal and bacterial communities were more pronounced in maturing pea and sugar beet plants. This detailed study demonstrates that plant species select for specialized microbial communities that change in response to plant growth and plant inputs.

Actinobacterial community structure in soils receiving long-term organic and inorganic amendments

The impact of long-term organic and inorganic amendments on the actinobacterial community in soils was studied. Denaturing gradient gel electrophoresis patterns based on the V3 region of 16S rRNA suggested that there was no significant difference between the communities occurring in the different amendments. However, analysis of the clone libraries of the actinobacterial communities by the use of multiple statistical approaches showed that these communities were significantly different from each other. Results showed that long-term organic and inorganic soil amendments did not significantly alter the overall phylogenetic diversity of the actinobacterial communities but did significantly change the community structure.

Enhanced diffusion of polycyclic aromatic hydrocarbons in artificial and natural aqueous solutions

Uptake of hydrophobic organic compounds into organisms is often limited by the diffusive transport through a thin boundary layer. Therefore, a microscale diffusion technique was applied to determine the diffusive mass transfer of 12 polycyclic aromatic hydrocarbons through water, air, surfactant solutions, humic acid solutions, aqueous soil and horse manure extracts, digestive fluid of a deposit-feeding worm, and root exudates from willow plants. In most cases the diffusive mass transfer of PAHs was much higher through the tested media than through water, and the enhancement factors increased with increasing hydrophobicity of the PAHs. The diffusive flux of benzo[a]pyrene was for instance enhanced 74 times through gut fluid of a deposit-feeding worm when compared to water. These findings demonstrate that a wide variety of dissolved organic carbon (DOC) at environmental levels can enhance diffusive mass transfer in various transport scenarios. The diffusive uptake of PAHs into sediment dwelling organisms is particularly efficient within the gut and at direct contract with the sediment matrix. Bioremediation might be enhanced bythe addition of auxiliary agents that enhance diffusive mass transfer. Enhanced diffusion needs also to be considered in dynamic transport models and for the operation and calibration of passive sampling techniques.

The use of microorganisms in ecological soil classification and assessment concepts

Microbial communities are integral parts of soil and their activity is very important to the functioning of soil. Therefore, microorganisms should be included in soil quality classification and assessment concepts. The challenges of using microbial indicators are to identify the best choice among the many techniques available to assess soil quality and to convert the information obtained from the microbial indicator into a form relevant for policy makers. In this article, we present a wide range of possible microbial indicators, some of them standardized; each provides slightly different information on soil quality. Experience with the use of indicators for assessment of microbial communities and soil quality is discussed. At present, as many microbial indicators as possible should be included to gain experience. At a minimum, measures of microbial biomass, respiration, and N mineralization and a community profiling method (e.g., DGGE, PLFA, or CLPP) should be included.

Genes involved in cyclic lipopeptide production are important for seed and straw colonization by Pseudomonas sp. strain DSS73

Survival in natural bulk soil and colonization of sugar beet seeds and barley straw residues were determined for Pseudomonas sp. strain DSS73 and Tn5 mutants in amsY (encoding a peptide synthetase involved in production of the cyclic lipopeptide amphisin) and gacS (encoding the sensory kinase of the two-component GacA/GacS regulatory system). No differences in survival or growth in response to carbon amendment (citrate) were observed in bulk soil. However, both mutants were impaired in their colonization of sugar beet seeds and barley straw residues by an inoculum established in the bulk soil. The two mutants had comparable colonization phenotypes, suggesting that amphisin production is more important for colonization than other gacS-controlled traits.

Using phospholipid fatty acid technique to study short-term effects of the biological control agent Pseudomonas fluorescens DR54 on the microbial microbiota in barley rhizosphere

The biological control agent (BCA) Pseudomonas fluorescens DR54 was applied to seeds (experiment 1) or roots (experiment 2) of barley growing in microcosms, while noninoculated plants served as controls. The fate of the BCA and its effects on the rhizosphere microbial community was evaluated in microcosms destructively sampled at days 2, 4, 6, and 9 after inoculation. In both experiments the number of P. fluorescens DR54 cells decreased immediately after application as enumerated by immunostaining and microscope direct counting. Substrate-induced respiration (SIR) was taken as a measurement of the active microbial biomass, while indicators of the total microbiota (and main taxonomic groups) were obtained using the phospholipid fatty acid (PLFA) technique. In experiment 1, these parameters were unaffected by the relatively small number of BCA cells applied, whereas in experiment 2, the larger BCA input resulted in an enhanced level of both SIR and PLFAs from Gram-negative bacteria (which included the BCA itself). However, at day 9 after inoculation, treatments with P. fluorescens DR54 and controls were similar in all measured parameters in both experiments. This was also illustrated very clearly by principal component analysis of the PLFA data, which in both experiments were able to discriminate between treatments in the first days after BCA inoculation, thus confirming the sensitivity of this method. Laccase activity has a potential as an indicator of fungal stress, e.g., when challenged with an antifungal BCA. This seemed to be supported in experiment 2, where the activity of this enzyme was enhanced four-fold in the BCA treatment at day 2. Our study shows that under the present conditions, P. fluorescens DR54 disappears from the soil and causes only transient effects on the soil microbiota. It also shows that the PLFA technique is a sensitive and reliable monitoring tool in in situ assessment of BCA nontarget effect on indigenous microorganisms in soil.

Bacterial diversity in agricultural soils during litter decomposition

Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.