Oligotrophic Bacteria Research Articles

Impacts of inorganic and organic fertilization treatments on bacterial and fungal communities in a paddy soil

Soil microbes play an integral role in agricultural production, and there is limited understating of the complex responses of microbial diversity to organic and conventional farming. Here we report the response of soil microbiome, of a paddy field, to ten years application of inorganic fertilizer (CF) and organic fertilizer (OF), also including a no fertilizer control (CK). The bacterial and fungal communities were examined using high-throughput sequencing. Our results revealed that compared with CK and OF, the CF treatment had lower richness of bacteria, but higher richness of fungi. To utilize the fertilizers efficiently and adaptions to soil conditions, bacterial and fungal compositions changed under different fertilizations. The application of CF increased the abundance of some oligotrophic bacteria such as Bacteroidetes and Acidobacteria, and increased the relative abundance of Zygomycota phylum of fungi. The application of OF increased the abundance of the copiotrophic bacteria such as Proteobacteria phylum, and the relative abundance of Agaricomycetes and Orbiliomycetes classes of fungi. The OF also had the sparsest and most discrete network indicated that soil microbes tended to be less interacted with each other after organic fertilizers inputs. This study suggested that the soil microorganisms respond differently to the inputs of inorganic and organic fertilizers in paddy soil, which offers novel insights into the potential of managing soil microbiomes for sustainable agricultural productivity.

Bacterial diversity and antibiotic resistances of abundant aerobic culturable bacteria in input and output samples of 15 German biogas plants.

Determination of the diversities and antibiotic resistances of the most abundant aerobic culturable bacteria and their survival in 15 German biogas plants (BGPs). Microbiological standard media (complex and selective media) were applied to enumerate mesophilic and oligotrophic bacteria (Enterobacteriaceae, Salmonella, staphylococci and enterococci) in input and output samples of BGPs. Concentrations of aerobic culturable bacteria in outputs were mostly one to two orders of magnitude lower than in input samples. In total, 852 isolates from input and 902 from output samples were identified either by partial 16S rRNA gene sequencing or Matrix-assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) analysis. Antibiotic resistance screening of target families against veterinary relevant antibiotics resulted in similar resistance pattern in input and output samples. Potentially pathogenic bacteria were detected in output samples of BGPs, but in decreased abundance. The selectivity of the most applied clinical standard media was insufficient. Only little is known about the release of antibiotic resistant and potentially pathogenic bacteria from BGPs. However, this study indicates the detection of several potentially pathogenic bacteria in output samples, which showed several antibiotic resistances.

Non-target effect of continuous application of chlorpyrifos on soil microbes, nematodes and its persistence under sub-humid tropical rice-rice cropping system

Application of pesticide in agricultural fields is “unnecessary evil” for non-target microflora and fauna. Hence, to identify the safer pesticide molecules against non-target microbes, a long-term pesticide experiment was initiated at National Rice Research Institute, Cuttack, India. In the present study, the effect of continuous application of chlorpyrifos (0.5kgha−1) in rice fields on non-target groups of soil microbes and nematodes was studied for seven seasons (four wet and three dry seasons) during 2009–2013. Treatments were arranged in a randomized complete block design with four replications of chlorpyrifos-treated (0.5kg a.i. ha−1) (CT) and untreated control (UT) plots. During seven seasons of experimentation, regular application of chlorpyrifos had no significant effect on population of heterotrophic aerobic, anaerobic, oligotrophic and copiotrophic bacteria in CT compared to UT, whereas, population of asymbiotic aerobic nitrogen fixer, nitrifiers, denitrifiers, gram positive and spore-forming bacteria were significantly reduced by nearly 0.25–2 fold in CT than UT. However, comparatively less deviation in population of actinomycetes, fungi, phosphate solubilizing and sulfur oxidizing bacteria were observed in CT than UT. Significant interactions were found between effects of chlorpyrifos with time in population dynamics of microbes. In plant parasitic nematode species, Meloidogyne graminicola (RRKN) and Hirschmanniella spp. (RRN), were significantly lower (p<0.01) in CT compared to UT after first year onwards. The overall observation of five years data indicated that the RRKN population showed a decreasing trend (R2=0.644) whereas RRN showed increasing trend (R2=0.932) in CT. The drastic chlorpyrifos dissipation was noticed after 15 days of application from the initial residue of 0.25mgkg−1 soil, which indicated that chlorpyrifos residue in rice field soil was not persistent and its half-life was found to be 4.02 days. Overall, the present findings revealed that non-target effect of repetitive application of chloropyrifos (0.5kgha−1) on soil microbes and nematodes was found less under rice-rice cropping system.

Bioprospecting of facultatively oligotrophic bacteria from non-rhizospheric soils

Conventional cultivation method relies on the use of nutrient-rich medium, which might limit the exploration of oligotrophic bacteria from soil ecosystems. In the present study attempts were made to isolate oligotrophic bacteria from non-rhizospheric samples collected from mountain roadside, beach, bay and wetland using 1000-fold diluted nutrient agar. Phylogenetic analysis and biogeographic studies of these isolates were performed based on their 16S rDNA sequences. Besides, tests for the utilization of methanol or agar as their carbon source (methylotrophic or agarolytic), light as their energy source (photoheterotrophic), fixation of nitrogen or solubilization of tricalcium phosphate were conducted. A total of 74 isolates with facultatively oligotrophic behavior were obtained, since they can proliferate on both 1000-fold diluted and conventional nutrient agar. 16S rDNA sequence analyses assigned them mainly to class Actinobacteria and α-Proteobacteria. All these isolates belonged to 24 genera which encompassed 35 species, demonstrating that these facultatively oligotrophic bacteria occupied a wide range of bacterial lineages. Fifty-seven out of 74 isolates formed colonies on methanol-containing agar, while only 21 showed better growth in methanol-containing medium. Nine isolates were verified to utilize agar instead of methanol for growth. A total of 4 isolates showed photoheterotrophic trait and the pufLM gene was successfully PCR amplified and sequenced. The methylotrophic or photoheterotrophic behaviors might provide advantages for them to inhabit oligotrophic environments. Members affiliated with many genera were first demonstrated to fix nitrogen or solubilize phosphate, and isolates with profound activities have potentials to be developed as bioinoculants used to promote plant growth. In addition, the use of diluted nutrient agar helped to explore several unrecognized species from non-rhizospheric soils. All these isolates may provide opportunities for studying their oligotrophic growth, metabolism and interaction with plants in a near future.

Response of microorganisms and enzymes to soil contamination with a mixture of pethoxamid terbuthylazine

This study analysed the effect of a mixture of pethoxamid (P) and terbuthylazine (T) contained in the herbicide Successor T 550 SE on organotrophic bacteria, total oligotrophic bacteria, Azotobacter and actinomycetes, oligotrophic sporulating bacteria, fungi and on the activities of dehydrogenases, catalase, urease, alkaline phosphatase, acid phosphatase, arylsulphatase and β-glucosidase. The phytotoxic effect of this pesticide on maize was also determined. The study was undertaken because of a lack of data concerning the effect of a P+T mixture on soil metabolism. The previously undertaken studies concerned only the separate effect of each of these substances. The P+T mixture disturbed soil homeostasis and altered soil stability, resulting in a succession of K-strategy organotrophic bacteria. It had a negative effect on bacteria of the genus Azotobacter, oligotrophic sporulating bacteria, actinomycetes and fungi, and a positive effect on oligotrophic bacteria. P+T in doses greater than 0.73 mg kg−1 of soil resulted in a strong inhibition of dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulphatase and β-glucosidase, and significantly inhibited the growth and development of maize.

Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity.

Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic–inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen–fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha diversity.

Pine sawdust as stimulator of the microbial community in post-arable afforested soil

ABSTRACTSawdust and wood residues are considered to be stimulators of microbiological change in soil and could be used in post-arable sites designed for afforestation. In this study, we discuss changes in bacteria numbers within selected groups in relation to soil type (arable and forest) and method of sawdust application. Sawdust was spread along planting rows and mixed with the soil or put directly under roots of planted seedlings. Applying sawdust under the roots increased the number of cellulolytic bacteria in all experimental treatments. On post-arable soil, adding sawdust in rows increased the number of copiotrophic bacteria and reduced the number of fluorescent bacteria and actinomycetes (ACT). In control forest soils, the number of copiotrophic, oligotrophic and spore-forming bacteria decreased simultaneously with increased ACT in all treatments. The number of fluorescent bacteria increased when sawdust was applied on forest sites under planted trees and decreased when sawdust was spread in planting rows. Oligotrophic bacteria also decreased in the latter case. We present a list of bacteria identified by DNA – 16S rRNA gene sequences. Adding sawdust to arable soils significantly changed the quantitative and qualitative composition of microbial communities.

Transcriptional Control in Marine Copiotrophic and Oligotrophic Bacteria with Streamlined Genomes.

Bacteria often respond to environmental stimuli using transcriptional control, but this may not be the case for marine bacteria such as "Candidatus Pelagibacter ubique," a cultivated representative of the SAR11 clade, the most abundant organism in the ocean. This bacterium has a small, streamlined genome and an unusually low number of transcriptional regulators, suggesting that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. Transcriptome sequencing during batch culture growth revealed that only 0.1% of protein-encoding genes appear to be under transcriptional control in Pelagibacter and in another oligotroph (SAR92) whereas >10% of genes were under transcriptional control in the copiotrophs Polaribacter sp. strain MED152 and Ruegeria pomeroyi When growth levels changed, transcript levels remained steady in Pelagibacter and SAR92 but shifted in MED152 and R. pomeroyi Transcript abundances per cell, determined using an internal RNA sequencing standard, were low (<1 transcript per cell) for all but a few of the most highly transcribed genes in all four taxa, and there was no correlation between transcript abundances per cell and shifts in the levels of transcription. These results suggest that low transcriptional control contributes to the success of Pelagibacter and possibly other oligotrophic microbes that dominate microbial communities in the oceans. Diverse heterotrophic bacteria drive biogeochemical cycling in the ocean. The most abundant types of marine bacteria are oligotrophs with small, streamlined genomes. The metabolic controls that regulate the response of oligotrophic bacteria to environmental conditions remain unclear. Our results reveal that transcriptional control is lower in marine oligotrophic bacteria than in marine copiotrophic bacteria. Although responses of bacteria to environmental conditions are commonly regulated at the level of transcription, metabolism in the most abundant bacteria in the ocean appears to be regulated by other mechanisms.

Sulfur Fertilization Changes the Community Structure of Rice Root-, and Soil- Associated Bacteria.

Under paddy field conditions, biological sulfur oxidation occurs in the oxidized surface soil layer and rhizosphere, in which oxygen leaks from the aerenchyma system of rice plants. In the present study, we examined community shifts in sulfur-oxidizing bacteria associated with the oxidized surface soil layer and rice roots under different sulfur fertilization conditions based on the 16S ribosomal RNA (rRNA) gene in order to explore the existence of oligotrophic sulfur-oxidizing bacteria in the paddy rice ecosystem. Rice plants were grown in pots with no fertilization (control) or CaCO3 or CaSO4 fertilization. A principal-coordinates analysis (PCoA) showed that CaSO4 fertilization markedly affected bacterial communities associated with rice roots and soil, whereas no significant differences were observed in plant growth among the fertilizer treatments examined. In rice roots, the relative abundance of Acidobacteria, Alphaproteobacteria, Gammaproteobacteria, and TM7 was significantly higher in CaSO4-fertilized pots than in control pots. Alphaproteobacteria, Bradyrhizobiaceae, and Methylocystaceae members were significantly more abundant in CaSO4-fertilized roots than in control roots. On the other hand, the abundance of Actinobacteria and Proteobacteria was lower in CaSO4-fertilized soil than in control soil. These results indicate that the bacteria associated with rice roots and soil responded to the sulfur amendment, suggesting that more diverse bacteria are involved in sulfur oxidation in the rice paddy ecosystem than previously considered.

Prevalence and Characterization of Putative Oligotrophic Bacteria in Fayoum Soils, Egypt

A variety of microbes can inhabit in extreme conditions. Extreme is a relative term which is viewed compared to what is normal for human beings. These microorganisms are known as oligotrophs. This work aimed to benefit from such organisms isolated from poor soils prevailing in fayoum Governorate. A survey of these organisms (specially) olignitrotrophs and oligocarbotrophs) was made on different soil samples. One hundred and twelve isolates were obtained from eight different soil sites. Ninety eight were obtained from NB/1000 (NB= nutrient broth) and fourteen from NB/10000 dilution. Fixed counts of the different isolates, when inoculated in NB medium with its different dilutions, were almost of constant counts for 30 days incubation at 30°C proved to be facultative not obligate oligotrophs. Eleven isolates produce IAA in amounts averaged 15 µg/ml and the rest were below 15 µg/ml. Five isolates only were capable to produce salyselic acids (S.A.) in appreciable amounts (< 100 µg/ml) and the rest was below 100 µg/ml. fifty four isolates solubilized zink (< 10 mm clear zone), and the rest was below 5 mm halo zone. Nine isolates solubilize phosphate (10mm clear zone) and the rest was below 5mm diameter. Fourty-seven isolates were able to fix nitrogen (olignitrotrophic) in medium deprived completely of N-source. Seventeen isolates were G- and the rest was G+. All isolates were oxidase and catalase positive but cannot ferment lactose. Most isolates were motile (95.5%), spore formers (76.6%) and all were short or long rods. Cellulase enzyme produced by seventeen and chitinase by five isolates only. All isolates examined were facultative oligotrophs as they grew on silica gel NB medium deprived of any source of carbon as well as on complete NB medium.

Heterotrophic and oligotrophic bacteria in preserved and intervened areas of the paramo the Cortadera, Boyacá, Colombia

Los paramos brindan servicios ambientales fundamentales a la poblacion, por la continua provision de agua, en cantidad y en calidad y el almacenamiento de carbono atmosferico, que ayuda a regular el calentamiento global. Estos ecosistemas estan sufriendo irreparables transformaciones, que controlan directa o indirectamente la estructura de las comunidades de microorganismos, cuya actividad es esencial para el mantenimiento de los ciclos biogeoquimicos. Se evaluo la diversidad de bacterias heterotrofas y oligotroficas, en los horizontes A, AB y B, de zonas conservadas y de zonas intervenidas en el Paramo de la Cortadera, en tres areas de muestreo, ubicadas en los municipios de Siachoque, Pesca y Toca. El numero de bacterias heterotrofas aerobicas totales y bacterias oligotroficas, se estimaron como unidades formadoras de colonias, sembrandose en Agar TSA + Nistatina y Agar MSC-MSH, a 30°C, por 48 horas. Los suelos tienen una textura franco arcilloso, con pH acido, bajo contenido de materia organica y altos niveles de P, aislandose los generos Pseudomonas, Acinetobacter, Lactobacillus , Bacillus y Klebsiella , y bacterias oligotroficas de los generos Caulobacter y Hyphomicrobium , siendo Pesca la zona mas diversa del Paramo de La Cortadera. Dicha diversidad podria estar influenciada por una amplia gama de factores bioticos y abioticos, que se puede ver afectada por cambios ambientales o alteraciones antropicas. Palabras clave: Diversidad, cultivos, antropico, horizontes, suelos.

Prokaryotes in Subsoil-Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks.

Microbial communities in soil provide a wide range of ecosystem services. On the small scale, nutrient rich hotspots in soil developed from the activities of animals or plants are important drivers for the composition of microbial communities and their functional patterns. However, in subsoil, the spatial heterogeneity of microbes with differing lifestyles has been rarely considered so far. In this study, the phylogenetic composition of the bacterial and archaeal microbiome based on 16S rRNA gene pyrosequencing was investigated in the soil compartments bulk soil, drilosphere, and rhizosphere in top- and in the subsoil of an agricultural field. With co-occurrence network analysis, the spatial separation of typically oligotrophic and copiotrophic microbes was assessed. Four bacterial clusters were identified and attributed to bulk topsoil, bulk subsoil, drilosphere, and rhizosphere. The bacterial phyla Proteobacteria and Bacteroidetes, representing mostly copiotrophic bacteria, were affiliated mainly to the rhizosphere and drilosphere—both in topsoil and subsoil. Acidobacteria, Actinobacteria, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia, bacterial phyla which harbor many oligotrophic bacteria, were the most abundant groups in bulk subsoil. The bacterial core microbiome in this soil was estimated to cover 7.6% of the bacterial sequencing reads including both oligotrophic and copiotrophic bacteria. In contrast the archaeal core microbiome includes 56% of the overall archaeal diversity. Thus, the spatial variability of nutrient quality and quantity strongly shapes the bacterial community composition and their interaction in subsoil, whereas archaea build a stable backbone of the soil prokaryotes due to their low variability in the different soil compartments.

Growth rates and rRNA content of four marine bacteria in pure cultures and in the Delaware estuary

Interpretation of 16S ribosomal RNA (rRNA) to 16S rRNA gene ratios (rRNA:rDNA) is based on a limited number of studies with rapidly growing copiotrophic bacteria. The most abundant bacteria in the ocean are oligotrophs, which probably grow more slowly than those bacteria whose rRNA:rDNA versus growth rate relationships are known. To examine whether rRNA:rDNA varies differently in oligotrophic marine bacteria than in copiotrophic bacteria, we used quantitative PCR and reverse transcriptase quantitative PCR to measure rRNA:rDNA in two marine copiotrophs and in two marine oligotrophs, including Candidatus Pelagibacter ubique HTCC1062, a coastal isolate of SAR11, the most abundant bacterial clade in the ocean. The rRNA:rDNA ratios for the two copiotrophs were similar to those expected on the basis of an analysis of previously studied copiotrophic bacteria, while the ratios for the two oligotrophs were substantially lower than predicted even given their slow growth rates. The rRNA:rDNA ratios determined along a transect in the Delaware estuary suggested that SAR11 bacteria grow at rates close to the growth rate in culture, while rates of the two copiotrophs were far below those observed in laboratory cultures. Our results have implications for interpreting rRNA:rDNA from natural communities, understanding growth strategies and comparing regulatory mechanisms in copiotrophs and oligotrophs.

The effect of carfentrazone-ethyl on soil microorganisms and soil enzymes activity / Wpływ karfentrazonu etylu na mikroorganizmy i aktywność enzymów glebowych

Abstract The aim of this study was to determine the effect of carfentrazone-ethyl (CE) doses of 0.265, 5.280, 10.560, 21.180, 42.240 μg kg-1 soil DM on fungi, Acnomycetes, organotrophic bacteria, total oligotrophic bacteria and spore-forming oligotrophic bacteria, and on the activity of dehydrogenases, catalase, urease, alkaline phosphatase, acid phosphatase, arylsulfatase and β-glucosidase. Carfentrazone-ethyl had a stimulating effect on total oligotrophic bacteria and organotrophic bacteria, but it inhibited the growth of Azotobacter, fungi, spore-forming oligotrophic bacteria and Actinomycetes. The analyzed substance modified the structure of soil microbial communities, and it induced the most profound changes in fungi. The highest values of the colony development (CD) index and the eco-physiological (EP) index were observed in organotrophic bacteria. The optimal dose of carfentrazone-ethyl stimulated the activity of dehydrogenases, catalase, urease, alkaline phosphatase, acid phosphatase and β-glucosidase, but it had no effect on arylsulfatase. The highest doses of the analyzed substance inhibited the activity of dehydrogenases (reduction from 11.835 to 11.381 μmol TPF), urease (reduction from 0.545 to 0.500 mmol N-NH4) and arylosulfatase (reduction from 0.210 to 0.168 mmol PNP). Dehydrogenases were most resistant to CE, whereas acid phosphatase and arylsulfatase were least resistant to the analyzed compound

Soil health indicators and Fusarium wilt suppression in organically and conventionally managed greenhouse soils

Soil health has been associated with internal cycling of nutrients, microbial activity and diversity as well as root disease suppression, which are frequently greater in organically than in conventionally managed soils. Resistance and resilience, measured as amplitude and frequency of oscillations in bacterial communities after a disturbance, were suggested as integral indicators of soil health, but until now there is little proof for this hypothesis. In this study, resistance and resilience of microbial communities and 24 soil chemical and biological parameters were analyzed and correlated to suppression of flax wilt (caused by Fusarium oxysporum f.sp. lini) in three experiments. Soil samples were collected on three different dates from a recently converted organic greenhouse and a similar, neighboring greenhouse under conventional management. The dynamics of copiotrophic and oligotrophic bacteria after a disturbance were monitored, and the resistance and resilience were calculated. The organic soil showed significantly higher water-holding capacity, organic matter content, total C and N contents, C:N ratio of the small particulate organic matter fraction, microbial biomass carbon, oxygen uptake rate, copiotrophic and oligotrophic bacterial communities and suppression of flax wilt incidence. After incorporation of a grass–clover mixture in both soils, the densities of copiotrophic and oligotrophic bacteria oscillated over time. The relative amplitudes of the oscillations (in grass–clover amended over non-amended soil) and the frequencies of the oscillations of both trophic groups were lower for the organic soil, indicating that the resistance and resilience of the microbial community were greater in this soil. These results support the hypothesis that the bacterial response to a disturbance can serve as an integral indicator for soil health, including disease suppressiveness.

Whole-Genome Sequences of Five Oligotrophic Bacteria Isolated from Deep within Lechuguilla Cave, New Mexico.

Here, we report the whole-genome sequences and annotation of five oligotrophic bacteria from two sites within the Lechuguilla Cave in the Carlsbad Caverns National Park, NM. Three of the five genomes contain an acyl-homoserine lactone signal synthase ortholog (luxI) that is involved in cell-to-cell communication via quorum sensing.

Microbial and enzymatic activity of soil contaminated with a mixture of diflufenican + mesosulfuron-methyl + iodosulfuron-methyl-sodium.

The aim of this study was to determine the effect of three active substances, diflufenican, mesosulfuron-methyl and iodosulfuron-methyl-sodium, applied in combination, on soil microbial counts, the structure of soil microbial communities, activity of soil enzymes and their resistance to the tested product, the biochemical indicator of soil fertility, and spring wheat yield. Soil samples with the granulometric composition of sandy loam with pHKCl 7.0 were used in a pot experiment. The herbicide was applied to soil at seven doses: 0.057 (dose recommended by the manufacturer), 1.140, 2.280, 4.560, 9.120, 18.240 and 36.480 mg kg−1 soil DM. Uncontaminated soil served as the control treatment. It was found that a mixture of the tested active substances increased the counts of total oligotrophic bacteria and spore-forming oligotrophic bacteria, organotrophic bacteria and actinomycetes, decreased the counts of Azotobacter and fungi, and modified the structure of soil microbial communities. The highest values of the colony development (CD) index and the ecophysiological (EP) index were observed in fungi and organotrophic bacteria, respectively. The herbicide applied in the recommended dose stimulated the activity of catalase, urease and acid phosphatase, but it had no effect on the activity of dehydrogenases, alkaline phosphatase, arylsulfatase and β-glucosidase. The highest dose of the analyzed substances (36.480 mg kg−1) significantly inhibited the activity of dehydrogenases, acid phosphatase, alkaline phosphatase and arylsulfatase. The values of the biochemical soil fertility indicator (BA21) decreased in response to high doses of the herbicide. Urease was most resistant and dehydrogenases were least resistant to soil contamination with a mixture of diflufenican + mesosulfuron-methyl + iodosulfuron-methyl-sodium. The analyzed herbicide had an adverse influence on spring wheat yield, and doses of 18.240 and 36.480 mg kg−1 led to eventual death of plants.

Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla

Agricultural practices affect the soil ecosystem in multiple ways and the soil microbial communities represent an integrated and dynamic measure of soil status. Our aim was to test whether the soil bacterial community and the relative abundance of major bacterial phyla responded predictably to long-term organic amendments representing different carbon qualities (peat and straw) in combination with nitrogen fertilization levels and if certain bacterial groups were indicative of specific treatments. We hypothesized that the long-term treatments had created distinctly different ecological niches for soil bacteria, suitable for either fast-growing copiotrophic bacteria, or slow-growing oligotrophic bacteria. Based on terminal-restriction fragment length polymorphism of the 16S rRNA genes from the total soil bacterial community and taxa-specific quantitative real-time PCR of seven different groups, all treatments significantly affected the community structure, but nitrogen fertilization was the most important driver for changes in the relative abundances of the studied taxa. According to an indicator species analysis, the changes were largely explained by the decline in the relative abundances of Acidobacteria, Gemmatimonadetes and Verrucomicrobia with nitrogen fertilization. Conditions more favourable for copiotrophic life strategies were indicated in these plots by the decreased metabolic quotient, i.e. the ratio between basal respiration rate and soil biomass. Apart from the Alphaproteobacteria that were significantly associated with peat, no taxa were indicative of organic amendment in general. However, several significant indicators of both peat and straw were identified among the terminal restriction fragments suggesting that changes induced by the organic amendments were mainly manifested at a lower taxonomical level. Our findings strengthen the proposition that certain higher bacterial taxa adapt in an ecologically coherent way in response to changes induced by fertilization.

Interactions of Heterotrophic Bacteria from Recycled Greenhouse Irrigation Water with Plant Pathogenic Pythium

Heterotrophic bacteria present in recycled greenhouse irrigation water (RIW) were characterized and then evaluated for their effect on Pythium aphanidermatum, P. cryptoirregulare, and P. irregulare. Nutrient agar (NA) and R2A agar were used to isolate copiotrophic and oligotrophic bacteria. Bacterial isolates recovered from RIW were categorized according to whether they inhibited Pythium growth, attached to hyphae, or enhanced Pythium growth in the three Pythium species used. Three bacterial isolates were selected to determine whether their in vitro interactions with Pythium aphanidermatum, the most pathogenic of the three species used, influenced disease development in the greenhouse. An isolate of Sphingobium sp. that inhibited Pythium, Pseudomonas sp. that attached to hyphae, and Cupriavidus sp. that enhanced the growth of P. aphanidermatum in vitro were used in greenhouse experiments to examine their effects on disease development in geranium (Pelargonium ×hortorum ‘White Orbit’) grown in pasteurized potting mix in ebb and flood irrigation systems. Disease progress curves evaluating the effect of each bacterium indicate that they did not suppress or enhance disease development (P = 0.05). Thus, the effects that the bacterial isolates had in vitro differed from their effects under greenhouse conditions.

Towards deconfounding hydrological and seasonal temperature variability in the determination of selected limnological variables of a temperate floodplain ecosystem

AbstractThis paper presents a methodological approach that can aid the assessment of variation in limnological variables in response to hydrological phases and seasonal temperature variation. The investigation was conducted in the Danube River floodplain, Kopački Rit, Croatia. The proposed approach facilitates a more accurate examination of the effects of first factor, while maintaining second factor less variable, and vice versa. Samples were collected in the floodplain channel and lake along a temporal connectivity gradient, and were grouped according to three hydrological phases (isolation, flow pulse and flood pulse) and according to three seasons (spring, summer and autumn). A permutational multivariate analysis of variance was used to analyse the hydrological effects within seasons, as well as seasonal effects within hydrological phases on selected limnological variables: pH, conductivity, dissolved oxygen, nitrites, nitrates, ammonium, total Kjeldahl nitrogen, total phosphorus, chlorophyll a concentrations and ratio of copiotrophic to oligotrophic bacteria. A multivariate data cloud was structured by hydrological phases during all investigated seasons, but not by all seasons during different hydrological phases. The strongest impact of hydrological phases on limnological variables occurred during summer. Seasonal effects were significant during the isolation and the flood pulse phases. The flow pulse phase somehow obscured the effects of seasonal change, resulting in temporal floodplain homogenization. One possible explanation is that water temperature determines potential limnological conditions, whereas hydrology determines actual conditions. Such results must be taken into account if the accurate effects of hydrology and seasonal change are to be assessed in temperate floodplain ecosystems. Copyright © 2014 John Wiley &amp; Sons, Ltd.