Response of the microbial community to copper oxychloride in acidic sandy loam soil

Acetaminophen Levels Found in Recycled Wastewater Alter Soil Microbial Community Structure and Functional Diversity

The practice of using recycled wastewater (RWW) has been successfully adopted to address the growing demand for clean water. However, chemicals of emerging concern (CECs) including pharmaceutical products remain in the RWW even after additional cleaning. When RWW is used to irrigate crops or landscapes, these chemicals can enter these and adjacent environments. Unfortunately, the overall composition and concentrations of CECs found in different RWW sources vary, and even the same source can vary over time. Therefore, we selected one compound that is found frequently and in high concentrations in many RWW sources, acetaminophen (APAP), to use for our study. Using greenhouse grown eggplants treated with APAP concentrations within the ranges found in RWW effluents, we investigated the short-term impacts of APAP on the soil bacterial population under agricultural settings. Using Illumina sequencing-based approaches, we showed that APAP has the potential to cause shifts in the microbial community most likely by positively selecting for bacteria that are capable of metabolizing the breakdown products of APAP such as glycosides and carboxylic acids. Community-level physiological profiles of carbon metabolism were evaluated using Biolog EcoPlate as a proxy for community functions. The Biolog plates indicated that the metabolism of amines, amino acids, carbohydrates, carboxylic acids, and polymers was significantly higher in the presence of APAP. Abundance of microorganisms of importance to plant health and productivity was altered by APAP. Our results indicate that the soil microbial community and functions could be altered by APAP at concentrations found in RWW. Our findings contribute to the knowledge base needed to guide policies regulating RWW reuse in agriculture and also highlight the need to further investigate the effects of CECs found in RWW on soil microbiomes.

Detection of Carbapenem-Resistance Genes in Klebsiella Species Recovered from Selected Environmental Niches in the Eastern Cape Province, South Africa

Carbapenemase-producing Enterobacteriaceae (CPE) have been heavily linked to hospital acquired infections (HAI) thereby leading to futility of antibiotics in treating infections and this have complicated public health problems. There is little knowledge about carbapenemase-producing Klebsiella spp. (CPK) in South Africa. This study aimed at determining the occurrence of CPK in different samples collected from selected environmental niches (hospitals, wastewater treatment plants, rivers, farms) in three district municipalities located in the Eastern Cape Province, South Africa. Molecular identification and characterization of the presumptive isolates were determined using polymerase chain reaction (PCR) and isolates that exhibited phenotypic carbapenem resistance were further screened for the possibility of harbouring antimicrobial resistance genes. One hundred (43%) of the 234 confirmed Klebsiella spp. isolates harboured carbapenem-resistance genes; 10 isolates harboured blaOXA-48-like; 17 harboured blaKPC; and 73 isolates harboured blaNDM-1. The emergence of blaKPC, blaOXA-48-like, and blaNDM-1 carbapenem-resistance genes in Klebsiella species associated with environmental sources is of great concern to public health.

Heavy Metal Threats to Plants and Soil Life in Southern Africa: Present Knowledge and Consequences for Ecological Risk Assessment

In recent times there has been remarkable development in the field of soil ecotoxicology and risk assessment (RA) models. It is, however, debatable if these RA models are robust representatives for worldwide relevance. In order to investigate this, the current overview aims to address heavy metal threats to soil life in southern Africa by investigating present knowledge and consequences for RA using research in southern Africa as a case. To this end, the focus is on southern African soils, soil life and living conditions. To critically discuss these issues, we report on extensive research conducted in the southern African context and looked how comparable these findings are to RA models employed in the western world. This is done by providing an inventory of selected studies focused on the ecotoxicity of metals towards soil life. It is concluded that there is a dearth of information on southern African soil life, most of which are laboratory-based studies carried out by a handful of researchers. Future research incorporating the available information into a soil ecosystem assessment procedure is paramount. It is recommended that a starting point to tackle this might be the development of holistic sight-specific guidelines for ecological risk assessment at larger spatial scales (km²) which takes into cognizance landscapes, vegetation and faunal characteristics.

Combining Different Potato-Associated Pseudomonas Strains for Improved Biocontrol of Phytophthora infestans

Late blight caused by Phytophthora infestans is considered as the most devastating disease of potato and is a re-emerging problem worldwide. Current late blight control practices rely mostly on synthetic fungicides or copper-based products, but growing awareness of the negative impact of these compounds on the environment has led to the search for alternative control measures. A collection of Pseudomonas strains isolated from both the rhizosphere and the phyllosphere of potato was recently characterized for in vitro protective effects against P. infestans. In the present study, we used a leaf disk assay with three different potato cultivars to compare the disease inhibition capacity of nine selected Pseudomonas strains when applied alone or in all possible dual and triple combinations. Results showed a strong cultivar effect and identified strains previously thought to be inactive based on in vitro assays as the best biocontrol candidates. One strain was much more active alone than in combination with other strains, while two other strains provided significantly better protection in dual combination than when applied alone. A subset of five strains was then further selected to determine their mutual influence on each other's survival and growth, as well as to characterize their activity against P. infestans in more details. This revealed that the two strains whose dual combination was particularly efficient were only weakly interfering with each other's growth and had complementary modes of action. Our results highlight the potential to harness the crop's native rhizosphere and phyllosphere microbiome through re-assembling strains with differing modes of action into small communities, thereby providing more consistent protection than with the application of single strains. We consider this as a first step toward more elaborate microbiome management efforts, which shall be integrated into global strategies for sustainable control of potato late blight.

In Vitro effects of various xenobiotics on Azotobacter chroococcum strains isolated from soils of southern Poland

Fourteen Azotobacter chroococcum strains isolated from soils of Southern Poland were studied concerning resistance to various xenobiotics: heavy metal ions: Cd(2+,) Cu(2+), Fe(3+), Mn(2+), Pb(2+), Zn(2+), pesticides: herbicides linuron (3-(3,4-dichlorophenyl)-1-methoxy-1-methylurea) and combination of mecoprop ((RS)-2-(4-chloro-2-methylphenoxy)propanoic acid), dicamba (3,6-dichloro-2-methoxybenzoic acid) and MCPA (2-methyl-4-chlorophenoxyacetic acid), fungicide copper oxychloride, insecticide fenitrothion (O,O-Dimethyl O-(3-methyl-4-nitrophenyl) phosphorothioate) and eight antibiotics commonly used against Gram-negative bacteria. The tested soils were divided into seven groups of land use: forest, field crop, park, urban lawn, industrial area, garden and fallow land, and were analyzed for the following heavy metal ion concentrations using the atomic absorption spectrometry (AAS) technique: Cd(2+,) Cu(2+), Fe(3+), Mn(2+), Pb(2+), Zn(2+). All strains were resistant to Pb(2+), whereas other metals caused the growth inhibition of the analyzed strains. There was no significant relationship between metal concentrations in the analyzed soils and metal resistance of the isolates. Herbicide linuron did not inhibit the growth of A. chroococcum in any of the concentrations. All other pesticides caused the growth inhibition only in the concentrate forms. All isolates were sensitive to β-lactam antibiotic Meropenem, however high intraspecies differentiation was observed concerning resistance to other antibiotics. The obtained results require further study regarding resistance mechanisms and possible use of the xenobiotic-resistant strains in land rehabilitation.

Radioecological risk assessment of low selenium concentrations through genetic fingerprints and metabolic profiling of soil bacterial communities

In a context of environmental risk assessment of nuclear (79)Se radionuclide, the impact of low Se-selenite concentrations (0.008 and 8 mg kg(-1)) on bacterial communities of two soils, a silty clay loam and a sandy soil, was investigated over a 6-month incubation time. This Se-selenite was partially labelled with (75)Se. The state of the Se-impacted bacterial communities was analyzed through total bacterial counts, DNA fingerprints (ARISA profiles) and metabolic profiling (carbon substrate utilization patterns). Furthermore, the genetic diversity of bacterial populations involved in Se volatilization was evaluated by tpm (thiopurine methyltransferase gene) profiling. Emissions of (75)Se and CaCl(2)-extractable (75)Se were measured by γ-spectrometry and scintillation analysis. Se-selenite inputs changed transiently the substrate utilization patterns of bacterial communities but did not affect the other indicators. Se volatilization was at its highest level just after adding Se-selenite and for about 1 week. This volatilization was proportional to the added Se-selenite concentrations. It was 100-fold higher in silty clay loam, even though Se bioavailability was reduced in this soil. The soils were amended with crushed grass 3 months after the addition of Se-selenite. This organic amendment affected the organization of bacterial communities and increased the Se-volatilizing activities of both soils. Original soil organic carbon and bacterial diversity and activities seemed responsible for the different levels of Se emissions observed in soils. tpm lineages, encoding Se methyltransferases, were detected in both soils, confirming the broad distribution of tpm-harbouring bacteria and their probable role in the emissions of volatile Se. Five distinct groups of tpm were recorded per soil, with tpmI lineage being detected throughout the incubation period. This study demonstrates the ability of bacterial communities at volatilizing Se concentrations inferior to geochemical backgrounds and suggests that a probable transfer of nuclear Se will occur through volatilization after an environmental spill.

Diversity and activity of free-living nitrogen-fixing bacteria and total bacteria in organic and conventionally managed soils

Agricultural soils are heterogeneous environments in which conditions affecting microbial growth and diversity fluctuate widely in space and time. In this study, the molecular ecology of the total bacterial and free-living nitrogen-fixing communities in soils from the Nafferton Factorial Systems Comparison (NFSC) study in northeast England were examined. The field experiment was factorial in design, with organic versus conventional crop rotation, crop protection, and fertility management factors. Soils were sampled on three dates (March, June, and September) in 2007. Total RNA was extracted from all soil samples and reverse transcribed. Denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were used to analyze nifH and 16S rRNA genes in order to study free-living diazotrophs and the total bacterial community, respectively. Crop rotation was shown to have a significant effect on total bacterial diversity (and that of free-living N fixers) (P ≤ 0.001). On all three dates, nifH activity was higher in the conventional crop rotation. In contrast, qPCR analysis of free-living N fixers indicated significantly higher levels of activity in conventionally fertilized plots in June (P = 0.0324) and in plots with organic crop protection in September (P = 0.0143). To our knowledge, the effects of organic and conventional farming systems on free-living diazotrophs have never been studied. An increased understanding of the impacts of management practices on free-living N fixers could allow modifications in soil management practices to optimize the activity of these organisms.

Effects of small increases in copper levels on culturable basidiomycetous yeasts in low-nutrient soils

AIMS

Investigating the effect of perturbations, with relatively low Cu concentrations, on yeast community composition in low-nutrient virgin soil.

METHODS AND RESULTS

Culturable soil yeast populations were monitored at an experimental site treated with the fungicide copper oxychloride (10 mg Cu per kg soil). Yeast numbers were unaffected by additional Cu; however, a shift in yeast community composition from Hymenomycetes to Urediniomycetes species occurred. Subsequent growth experiments conducted with a synthetic liquid medium revealed that hymenomycetous and urediniomycetous yeasts were affected differently by 1 and 10 mg l(-1) Cu. Soil microcosm experiments then indicated that additional 10 mg kg(-1) Cu may improve the competitive ability of urediniomycetous yeasts in the presence of hymenomycetous yeasts.

CONCLUSIONS

The shift from hymenomycetous to urediniomycetous yeasts, as a result of slightly increased soil Cu levels, may be because of hymenomycetous yeasts being more sensitive to elevated Cu levels and urediniomycetous yeasts having an improved competitive ability in the presence of elevated Cu levels.

SIGNIFICANCE AND IMPACT OF THE STUDY

Yeast community composition of pristine low-nutrient soils may change as a result of perturbations with relatively low concentrations of Cu. Urediniomycetous yeasts should be studied as potential bio-indicators of Cu perturbations.

Temporal bacterial diversity associated with metal-contaminated river sediments

The temporal activity, abundance and diversity of microbial communities were evaluated across a metal-contamination gradient around a Superfund site in Montana. In order to analyze short-term variability, samples were collected from six sites on four occasions over 12 months. Measurements of community activity, diversity and richness, quantified by dehydrogenase activity and through denaturant gradient gel electrophoresis (DGGE), respectively, were higher at contaminated sites adjacent to the smelter, relative to reference sites. 16S rRNA gene copy numbers, measured by quantitative PCR, showed seasonal variability, yet were generally higher within polluted sediments. Jaccard similarity coefficients of DGGE profiles, found sites to cluster based primarily on geographical proximity rather than geochemical similarities. Intra-site clustering of the most polluted sites also suggests a stable metal-tolerant community. Sequences from DGGE-extracted bands were predominantly Beta and Gammaproteobacteria, although the communities at all sites generally maintained a diverse phylogeny changing in composition throughout the sampling period. Spearman's rank correlations analysis found statistically significant relationships between community composition and organic carbon (r-value = 0.786) and metals (r-values As = 0.65; Cu = 0.63; Zn = 0.62). A diverse and abundant community at the most polluted site indicates that historical contamination selects for a metal-resistant microbial community, a finding that must be accounted for when using the microbial community within ecosystem monitoring studies. This study highlights the importance of using multiple time-points to draw conclusions on the affect of metal contamination.

Evidence of symbiosis between the soil yeast Cryptococcus laurentii and a sclerophyllous medicinal shrub, Agathosma betulina (Berg.) Pillans

The interaction between a common soil yeast, Cryptococcus laurentii, and a slow-growing medicinal plant adapted to low-nutrient soils, Agathosma betulina (Berg.) Pillans, was studied. C. laurentii CAB 578 was isolated from the rhizosphere of wild A. betulina, and liquid chromatography-tandem mass spectrometry (LC-MS-MS) analysis revealed that the yeast was capable of producing polyamines, such as cadaverine and spermine, while growing in vitro in a chemically defined medium. Since the exogenous application of polyamines are known to impact on root growth, these findings supported the results obtained when axenic cultures of A. betulina seedlings were inoculated with C. laurentii CAB 578 and cultivated for 5 months under glasshouse conditions. The presence of the yeast increased root growth by 51%. Using soil dilution plates, it was demonstrated that yeast numbers were greater in the vicinity of the roots than in the bulk soil. In addition, fluoromicroscopy, in combination with the fluorescent probes Fungolight and Calcofluor white, revealed the presence of metabolic active yeast colonies on the rhizoplane 5 months after initiation of the experimentation. The study provided evidence for a symbiosis between C. laurentii and A. betulina.

Soil properties that impact yeast and actinomycete numbers in sandy low nutrient soils

To explore the beneficial qualities or detrimental consequences of cultureable soil yeasts, it is important to understand which physicochemical soil properties most impact populations of these unicellular fungi in their natural habitat. The goal of this study was to determine which soil properties dictate yeast numbers in pristine sandy, low nutrient soils within a semi-arid region. A correlation matrix of the data obtained for 19 different environmental variables indicated a negative correlation between soil pH and yeast numbers. Using general regression models, it was demonstrated that soil pH and copper concentration were the 2 variables that correlated best with soil yeast counts in these soils. However, soil moisture content was found to be the environmental factor with the most impact on cultureable actinomycetes and heterotrophic microbes. The study also demonstrated that divalent cation availability might impact the size of both yeast and prokaryote populations in these soils.