Multiplex PCR for Assessment of Tetracycline Resistance (tet) Genes in Antibiotic-Resistant Soil Bacteria and the Ecological Implications

Antibiotics are becoming increasingly prevalent in bacterial communities due to clinical and agricultural misuse and overuse in their environment. As exposure increases, so does the incidence of microbial resistance. Such is the case with bacterial resistance to tetracyclines, a phenotype often acquired through the horizontal gene transfer of tet genes between bacteria. The objective of this project was to analyze the bacterial diversity of tet resistance genes in soil from Miami-Dade County. Bacterial isolates were Gram-stained and the Kirby-Bauer antibiotic disk diffusion test was performed to determine each bacterium’s degree of resistance. The 16S rRNA gene from antibiotic-resistant isolates was amplified by PCR and sequenced to identify the isolates. All isolates’ tet genes were amplified by multiplex PCR, sequenced, and compared. Among eight isolates, three distinct species were positively identified based on their 16S rRNA sequences and four distinct tet genes were identified, though all tested susceptible to tetracycline via the Kirby-Bauer test. This project clarifies some aspects of the ecology of antibiotic resistance genes, their natural ecological function and the potential for the expansion of intrinsic multi-antibiotic resistance into new ecosystems and/or hosts.

Biogeochemical Effects of Simulated Sea Level Rise on Carbon Loss in an Everglades Mangrove Peat Soil

Saltwater intrusion and inundation can affect soil microbial activity, which regulates the carbon (C) balance in mangroves and helps to determine if these coastal forests can keep pace with sea level rise (SLR). This study evaluated the effects of increased salinity (+15 ppt), increased inundation (−8 cm), and their combination, on soil organic C loss from a mangrove peat soil (Everglades, Florida, USA) under simulated tides. Soil respiration (CO2 flux), methane (CH4) flux, dissolved organic carbon (DOC) production, and porewater nutrient concentrations were quantified. Soil respiration was the major pathway of soil organic C loss (94–98%) and was approximately 90% higher in the control water level than the inundated treatment under elevated salinity. Respiration rate increased with water temperature, but depended upon salinity and tidal range. CH4 flux was minimal, while porewater DOC increased with a concomitant, significant decline in soil bulk density under increased inundation. Porewater ammonium increased (73%) with inundation and soluble reactive phosphorus increased (32%) with salinity. Overall, the decline in soil organic C mineralization from combined saltwater intrusion and prolonged inundation was not significant, but results suggest SLR could increase this soil’s susceptibility to peat collapse and accelerate nutrient and DOC export to adjacent Florida Bay.

Effect of Water Management on Interannual Variation in Bulk Soil Properties from the Eastern Coastal Everglades

We examined interannual variation in soil properties from wetlands occurring in adjacent drainage basins from the southeastern Everglades. Triplicate 10-cm soil cores were collected, homogenized, and analyzed during the wet season 2006–2010 from five freshwater sawgrass wetland marshes and three estuarine mangrove forests. Soil bulk density from the Taylor Slough basin ranged from 0.15 gm-cm−3 to 0.5 gm-cm−3, was higher than from the Panhandle basin every year, and generally increased throughout the study period. Organic matter as a percent loss on ignition ranged from 7 % to 12 % from freshwater marshes and from 13 % to 56 % from estuarine mangroves. Extractable iron in soils was similar among drainage basins and wetland types, typically ranging from 0.6 to 2.0 g Fe kg−1. In contrast, inorganic sulfur was on average over four times higher from estuarine soils relative to freshwater, and was positively correlated with soil organic matter. Finally total soil phosphorus (P) was lower in freshwater soils relative to estuarine soils (84 ± 5 versus 326 ± 32 mg P kg−1). Total P from the freshwater marshes in the Panhandle basin rose throughout the study period from 54.7 ± 8.4 to 107 ± 17 mg P kg−1, a possible outcome of differences in water management between drainage basins.

The Effect of Nutrient-Rich Effluents from Shrimp Farming on Mangrove Soil Carbon Storage and Geochemistry Under Semi-Arid Climate Conditions in Northern Brazil

A semi-arid mangrove estuary system in the northeast Brazilian coast (Ceará state) was selected for this study to (i) evaluate the impact of shrimp farm nutrient-rich wastewater effluents on the soil geochemistry and organic carbon (OC) storage and (ii) estimate the total amount of OC stored in mangrove soils (0–40 cm). Wastewater-affected mangrove forests were referred to as WAM and undisturbed areas as Non-WAM. Redox conditions and OC content were statistically correlated (P < 0.05) with seasonality and type of land use (WAM vs. Non-WAM). Eh values were from anoxic to oxic conditions in the wet season (from − 5 to 68 mV in WAM and from < 40 to > 400 mV in Non-WAM soils) and significantly higher (from 66 to 411 mV) in the dry season (P < 0.01). OC contents (0–40 cm soil depth) were significantly higher (P < 0.01) in the wet season than the dry season, and higher in Non-WAM soils than in WAM soils (values of 8.1 and 6.7 kg m− 2 in the wet and dry seasons, respectively, for Non-WAM, and values of 3.8 and 2.9 kg m− 2 in the wet and dry seasons, respectively, for WAM soils; P < 0.01). Iron partitioning was significantly dependent (P < 0.05) on type of land use, with a smaller degree of pyritization and lower Fe-pyrite presence in WAM soils compared to Non-WAM soils. Basal respiration of soil sediments was significantly influenced (P < 0.01) by type of land use with highest CO2 flux rates measured in the WAM soils (mean values of 0.20 mg CO2 h− 1–g− 1 C vs. 0.04 mg CO2 h− 1–g− 1 C). The OC storage reduction in WAM soils was potentially caused (i) by an increase in microbial activity induced by loading of nutrient-rich effluents and (ii) by an increase of strong electron acceptors [e.g., NO3−] that promote a decrease in pyrite concentration and hence a reduction in soil OC burial. The current estimated OC stored in mangrove soils (0–40 cm) in the state of Ceará is approximately 1 million t.

Selected soil properties and bacterial abundance in the glacier forefields 'Black Valley Transect' and 'Glacier Transect' on Larsemann Hills, East Antarctica

Antarctic glacier forefields are extreme environments and pioneer sites for ecological succession. Increasing temperatures due to global warming lead to enhanced deglaciation processes in cold-affected habitats, and new terrain is becoming exposed to soil formation and microbial colonization. However, only little is known about the impact of environmental changes on microbial communities and how they develop in connection to shifting habitat characteristics. In this study, using a combination of molecular and geochemical analysis, we determine the structure and development of bacterial communities depending on soil parameters in two different glacier forefields on Larsemann Hills, East Antarctica. Our results demonstrate that deglaciation-dependent habitat formation, resulting in a gradient in soil moisture, pH and conductivity, leads to an orderly bacterial succession for some groups, for example Cyanobacteria, Bacteroidetes and Deltaproteobacteria in a transect representing 'classical' glacier forefields. A variable bacterial distribution and different composed communities were revealed according to soil heterogeneity in a slightly 'matured' glacier forefield transect, where Gemmatimonadetes, Flavobacteria, Gamma- and Deltaproteobacteria occur depending on water availability and soil depth. Actinobacteria are dominant in both sites with dominance connected to certain trace elements in the glacier forefields.

(Table 1) Soil description of pits dug in coastal, inland and higland Antarctic Dry Valleys

In the past few years, it has become increasingly apparent that perchlorate (ClO4-) is present on all continents, except the polar regions where it had not yet been assessed, and that it may have a significant natural source. Here, we report on the discovery of perchlorate in soil and ice from several Antarctic Dry Valleys (ADVs) where concentrations reach up to 1100/µg/kg. In the driest ADV, perchlorate correlates with atmospherically deposited nitrate. Far from anthropogenic activity, ADV perchlorate provides unambiguous evidence that natural perchlorate is ubiquitous on Earth. The discovery has significant implications for the origin of perchlorate, its global biogeochemical interactions, and possible interactions with the polar ice sheets. The results support the hypotheses that perchlorate is produced globally and continuously in the Earth's atmosphere, that it typically accumulates in hyperarid areas, and that it does not build up in oceans or other wet environments most likely because of microbial reduction on a global scale.

Soil organic carbon storage and soil properties for 50 soil profiles in the Lena River Delta including land form description and map

To project the future development of the soil organic carbon (SOC) storage in permafrost environments, the spatial and vertical distribution of key soil properties and their landscape controls needs to be understood. This article reports findings from the Arctic Lena River Delta where we sampled 50 soil pedons. These were classified according to the U.S.D.A. Soil Taxonomy and fall mostly into the Gelisol soil order used for permafrost-affected soils. Soil profiles have been sampled for the active layer (mean depth 58±10 cm) and the upper permafrost to one meter depth. We analyze SOC stocks and key soil properties, i.e. C%, N%, C/N, bulk density, visible ice and water content. These are compared for different landscape groupings of pedons according to geomorphology, soil and land cover and for different vertical depth increments. High vertical resolution plots are used to understand soil development. These show that SOC storage can be highly variable with depth. We recommend the treatment of permafrost-affected soils according to subdivisions into: the surface organic layer, mineral subsoil in the active layer, organic enriched cryoturbated or buried horizons and the mineral subsoil in the permafrost. The major geomorphological units of a subregion of the Lena River Delta were mapped with a land form classification using a data-fusion approach of optical satellite imagery and digital elevation data to upscale SOC storage. Landscape mean SOC storage is estimated to 19.2±2.0 kg C/m**2. Our results show that the geomorphological setting explains more soil variability than soil taxonomy classes or vegetation cover. The soils from the oldest, Pleistocene aged, unit of the delta store the highest amount of SOC per m**2 followed by the Holocene river terrace. The Pleistocene terrace affected by thermal-degradation, the recent floodplain and bare alluvial sediments store considerably less SOC in descending order.

Tab. 1+2+3: Selected principal soil properties in the oil exploitation region of KomiArcticOil (Usinsk) in the Russian tundra

Oil polluted and not oil polluted soils (crude oil hydrocarbons contents: 20-92500 mg/kg dry soil mass) under natural grass and forest vegetation and in a bog in the Russian tundra were compared in their principal soil ecological parameters, the oil content and the microbial indicators. CFE biomass-C, dehydrogenase and arylsulfatase activity were enhanced with the occurrence of crude oil. Using these parameters for purposes of controlling remediation and recultivation success it is not possible to distinguish bctween promotion of microbial activity by oil carbon or soil organic carbon (SOC). For this reason we think that these parameters are not appropriate to indicate a soil damage by an oil impact. In contrast the metabolie quotient (qC02), calculated as the ratio between soil basal respiration and the SIR biomass-C was adequate to indicate a high crude oil contamination in soil. Also, the ß-glucosidase activity (parameter ß-GL/SOC) was correlated negatively with oil in soil. The indication of a soil damage by using the stress parameter qCO, or the specific enzyme activities (activity/SOC) minimizes the promotion effect of the recent SOC content on microbial parameters. Both biomass methods (SIR, CFE) have technical problems in application for crude oil-contaminated and subarctic soils. CFE does not reflect the low C_mic level of the cold tundra soils. We recommend to test every method for its suitability before any data collection in series as well as application for cold soils and the application of ecophysiological ratios as R_mic/C_mic, C_mic/SOC or enzymatic activity/SOC instead of absolute data.

Collection of measurements on physical soil properties in plots of the Jena Experiment (time series since 2002)

This collection contains measurements on physical soil properties of the plots of the different sub-experiments at the field site of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing

Soil porosity along a plant diversity gradient in the Jena Experiment (Main Experiment, 2013)

Soil porosity is the fraction of total volume occupied by pores or voids measured at matric potential 0. To measure soil porosity, soil samples were taken from each plot using sample rings with an internal diameter of 57 mm and height of 40.5 mm (inner volume of Vs=100 cm3). The samples were placed on a sand bed box with water level set to allow saturation of the samples with water. After 48 h the samples were weighed (ms), oven dried at 105 °C and weighed again to determine the dry weight (md). We calculated soil porosity (n [%]) using the density of water (?w=1 g cm?3), n=100 ? (mw-md) / (?w?Vs). To account for the spatial variation of soil properties, three replicates were taken per plot, approximately 2, 3 and 4 weeks after the flood that occurred at the field site during June 2013. Data are the average soil porosity values per plot. All data where measured in the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown in the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, or 4 functional groups). Plots were maintained by bi-annual weeding and mowing.

Redistribution of Soil Organic Matter by Permafrost Disturbance in the Canadian High Arctic

With increased warming in the Arctic, permafrost thaw may induce localized physical disturbance of slopes. These disturbances, referred to as active layer detachments (ALDs), redistribute soil across the landscape, potentially releasing previously unavailable carbon (C). In 2007–2008, widespread ALD activity was reported at the Cape Bounty Arctic Watershed Observatory in Nunavut, Canada. Our study investigated organic matter (OM) composition in soil profiles from ALD-impacted and undisturbed areas. Solid-state 13C nuclear magnetic resonance (NMR) and solvent-extractable biomarkers were used to characterize soil OM. Throughout the disturbed upslope profile, where surface soils and vegetation had been removed, NMR revealed low O-alkyl C content and biomarker analysis revealed low concentrations of solvent-extractable compounds suggesting enhanced erosion of labile-rich OM by the ALD. In the disturbed downslope region, vegetation remained intact but displaced material from upslope produced lateral compression ridges at the surface. High O-alkyl content in the surface horizon was consistent with enrichment of carbohydrates and peptides, but low concentrations of labile biomarkers (i.e., sugars) suggested the presence of relatively unaltered labile-rich OM. Decreased O-alkyl content and biomarker concentrations below the surface contrasted with the undisturbed profile and may indicate the loss of well-established pre-ALD surface drainage with compression ridge formation. However, pre-ALD profile composition remains unknown and the observed decreases may result from nominal pre-ALD OM inputs. These results are the first to establish OM composition in ALD-impacted soil profiles, suggesting reallocation of permafrost-derived soil C to areas where degradation or erosion may contribute to increased C losses from disturbed Arctic soils.

Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica

The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention, relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions.

In vitro experimental environments lacking or containing soil disparately affect competition experiments of Aspergillus flavus and co-occurring fungi in maize grains

In vitro experimental environments are used to study interactions between microorganisms, and predict dynamics in natural ecosystems. This study highlights that experimental in vitro environments should be selected to closely match the natural environment of interest during in vitro studies to strengthen extrapolations about aflatoxin production by Aspergillus and competing organisms. Fungal competition and aflatoxin accumulation was studied in soil, cotton wool or tube (water-only) environments, for Aspergillus flavus competition with Penicillium purpurogenum, Fusarium oxysporum or Sarocladium zeae within maize grains. Inoculated grains were incubated in each environment at two temperature regimes (25oC and 30oC). Competition experiments showed interaction between main effects of aflatoxin accumulation and environment at 25oC, but not so at 30oC. However, competition experiments showed fungal populations were always interacting with their environments. Fungal survival differed after the 72-hour incubation in different experimental environments. Whereas, all fungi incubated within the soil environment survived; in the cotton-wool environment, none of the competitors of A. flavus survived at 30 oC. With aflatoxin accumulation, F. oxysporum was the only fungus able to interdict aflatoxin production at both temperatures. This occurred only in the soil environment and fumonisins accumulated instead. Smallholder farmers in developing countries face serious mycotoxin contamination of their grains, and soil is a natural reservoir for the associated fungal propagules, and a drying and storage surface for grains on these farms. Studying fungal dynamics in the soil environment and other environments in vitro can provide insights into aflatoxin accumulation post harvest.

Influence of mucuna fallow crop on selected soil properties, weed suppression and taro yields in Taveuni, Fiji

Two field experiments were carried out in Taveuni, Fiji to study the effects of mucuna (Mucuna pruriens) and grass fallow systems at 6 and 12 month durations on changes in soil properties (Experiment 1) and taro yields (Experiment 2). Biomass accumulation of mucuna fallow crop was significantly higher (P<0.05) than grass fallow crop at both 6 and 12 month durations. The longer fallow duration resulted in higher (P<0.05) total soil organic carbon, total soil nitrogen and earthworm numbers regardless of fallow type. Weed suppression in taro grown under mucuna was significantly greater (P<0.05) than under natural grass fallow. Taro grown under mucuna fallow significantly outyielded taro grown under grass fallow (11.8 vs. 8.8 t ha-1). Also, the gross margin of taro grown under mucuna fallow was 52% higher than that of taro grown under grass fallow. © ISHS.

Environmental factors affecting soil metals near outlet roads in Poznan, Poland: impact of grain size, soil depth, and wind dispersal

We determined the Cd, Cr, Cu, Ni, Pb, and Zn concentrations in soil samples collected along the eight main outlet roads of Poznan. Samples were collected at distances of 1, 5, and 10 m from the roadway edges at depth intervals of 0-20 and 40-60 cm. The metal content was determined in seven grain size fractions. The highest metal concentrations were observed in the smallest fraction (<0.063 mm), which were up to four times higher than those in sand fractions. Soil Pb, Cu, and Zn (and to a lesser extent Ni, Cr, and Cd) all increased in relation to the geochemical background. At most sampling sites, metal concentrations decreased with increasing distance from roadway edges and increasing depth. In some locations, the accumulation of metals in soils appears to be strongly influenced by wind direction. Our survey findings should contribute in predicting the behavior of metals along outlet road, which is important by assessing sources for further migration of heavy metals into the groundwater, plants, and humans.