Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing

Heavy metal pollution of terrestrial and aquatic environments in Niger-delta region of Nigeria is on the increase due to increased urbanization and crude oil exploration. Tympanotonus fuscastus are mud dwellers and could bioaccumulate heavy metals; therefore consumption of heavy metal contaminated sea foods like periwinkle may breed lots of health problems. Heavy metal concentration in water, sediment and Periwinkle samples from three locations (Itu-River, Abuloma River and Oron River) in the Niger Delta Region of Nigeria were evaluated using atomic absorption flame photometry. Result showed that cadmium (Cd) concentration was highest in water samples from Abuloma River (0.106 mg/l) while lead (Pb) concentration was highest (0.01mg/l) in the water samples from Itu River. Cd and Pb concentrations (0.127 and 0.08 mg/kg, respectively) in sediment samples were highest in Abuloma River. The concentration of Cd in T. fuscastus samples was 0.11 mg/kg in Abuloma River, while concentration was 0.27 mg/kg in Oron River. Copper (Cu) was generally low in the water samples; the highest concentration (0.011 mg/kg) was obtained in water samples from Oron River. Sediment concentration of Cu was high (0.088 mg/kg) in Itu River, while its concentration in the periwinkle samples was 0.54 mg/kg in Abuloma River. The results also showed that Cr, As and Hg were below detectable concentration in tissues, soil and water samples from Itu and Abuloma Rivers, while Hg concentration in Oron River sediment was 64.2 mg/kg. Key words: Sea foods, heavy metals, pollution, environment, nutrition, bioaccumulation

The study was conducted to assess the levels of organochlorine (OC) pesticide residues in Lake TeKeze dam have been investigated using water, sediment and fish (Labeobarbusspp, Clariasgariepinus and Oreochromis niloticus) samples as a case study to find out the extent of pesticide contamination and accumulation in the lake. Six OC pesticides namely DDT, DDE, Lindane, Endosulfan, Heptachlor and Chlordane were analyzed in four sites at two seasons. Water samples were processed using a liquid-liquid extraction technique and gas chromatograph equipped with electron capture detector (GC-ECD). Soxhlet extraction was used for fish and sediment samples followed by clean up and gas chromatograph. DDE was the predominant residue in all the samples analyzed, at the mean concentrations of 0.052 ppb, 9.80 ppb and 4.81 ppb in water, sediment and fish samples, respectively. The lowest levels of OC pesticides were related to Heptachlor and Chlordane which none of them were found in water samples. It also indicated the extensive presence and usage of these pesticides in the study environment, which include recent use of this pesticide for agricultural purposes. Thus, the use of these pesticides to control pest by farmers within the study area with little or no knowledge must be checked through adequate control of the trade and use of pesticides and the enforcement of appropriate sanctions.

To determine whether Mycobacterium avium subsp paratuberculosis could be isolated from soil-pasture, faecal, water and sediment samples on farms before and after removal of sheep with paratuberculosis. A feasibility study and subsequent field survey. First the analytical sensitivity of radiometric culture of the organism from two types of soil was determined relative to faeces. Then soil-pasture, faecal, water and sediment samples were collected for culture from a range of sites from 6 farms with paratuberculosis affected sheep and goats. Similar samples were collected from 20 farms at least 9 months after removal of infected stock. The analytical sensitivity of culture of M a paratuberculosis from soil samples was 2 orders of magnitude less than that from faeces, and environmental samples required longer incubation periods to yield significant growth in radiometric culture (BACTEC) medium. However, the organism was recovered from approximately 20% of 163 soil-pasture, water and sediment samples from 6 properties with clinically-affected animals with paratuberculosis. The positive samples were from a range of topographic sites, including open exposed and dry areas, however, low lying areas tended to have larger numbers of organisms. When the same sites were sampled again about 5 months later, only 1 was culture positive, and none were culture positive > 12 months later. Of 17 water and dam sediment samples collected from farm 6, which had long-standing high prevalence OJD infection, only one water sample and one sediment from the same dam were culture positive. None of the 5 water samples from the other farms were culture positive. Of 96 water samples, 90 sediment samples and 93 soil samples from farms that had been destocked of infected sheep/goats for 9 to 24 months, one sediment sample from a farm in Victoria (destocked for 12 months) and two sediment samples from a farm in New South Wales (10, 19 months) were culture positive. Recontamination from cattle or water could not be excluded as a cause of the positive cultures from the second farm. M a paratuberculosis can be detected by radiometric culture in environmental samples from farms grazed by sheep or goats with paratuberculosis. There is a relatively low likelihood of recovery of the organism from water samples from such farms, and at 5 or more months after removing stock with paratuberculosis the likelihood of positive cultures from environmental samples is very low. Although the analytical sensitivity of culture from environmental samples is less than that from faeces, surveys of environmental sites are nevertheless feasible. However, improved culture methods are needed for critical surveys and to study the movement and fate of the organism in the environment.

This study investigated the circulation of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the Nha Phu and Bich Dam areas, the Nha Trang Sea, Vietnam, a region experiencing considerable environmental stress due to urbanization and tourism. Multidrug-resistant bacteria including Escherichia coli, Enterobacter hormaechei, Proteus mirabilis, Pseudomonas aeruginosa, Vibrio alginolyticus, Bacillus cereus, and Micrococcus luteus were detected in sediment and water samples. The abundance of marine microbiome was from 3.8 × 109 to 1.5 × 109 copies/mL in surface water samples and in the sediment and from 9.9 × 107 to 2.6 × 109 copies/g in sediments. Among the four target ARGs, the sul1 and sul2 genes associated with sulfonamides resistance were detected in both water and sediment samples ranging from 2.3 × 100 to 4.5 × 103 copies/mL, and from 2.0 × 103 to 4.7 × 105 copies/g in water and sediment samples, respectively. For tetracycline resistance, tetQ and tetM were detected in 60% and 100% studied samples. The abundance of these genes was up to 1.7 × 10² copies/mL in water samples, and 1.1 × 105 copies/g in sediments. The class 1 integron-integrase gene intI1 displayed from 6.2 × 10² to 2.6 × 10³ copies/mL and from 4.8 × 104 to 8.2 × 105 copies/g in water and sediment samples, respectively. Our findings emphasize the risk of ARB and their associated ARGs being transmitted in the marine environments of the Nha Trang Sea through the assistance of mobile genetic elements.

This study investigated the concentrations of Tributyltin (TBT) in water, sediment, and fish muscle samples taken from Kaohsiung Harbor and Kaoping River estuary, Taiwan. TBT concentrations in water and sediment samples ranged from less than 18.5 to 34.1 ng Sn L−1 and from 2.44 to 29.7 ng Sn g−1 weight per weight (w/w), respectively. Concentrations in the TBT‐contaminated fish muscle samples ranged from 10.8 to 79.6 ng Sn g−1 w/w. The TBT concentrations in fish muscle were higher than those in water and sediment samples. The fish muscle/water TBT bioconcentration factor (BCF) ranged from 590 to 3363 L kg−1. Additionally, the water samples were assessed for androgenic activity with an MCF7‐AR1 human breast cancer cell line. The androgenic activity ranged from 0.94 to 3.1 ng‐dihydrotestosterone per litre water (ng‐DHT L−1). Higher concentrations of TBT in water and sediment samples occurred in the dry season, but the androgenic activity had higher values in the rainy season.

The concentrations and distribution patterns of three typical pharmaceuticals and personal care products (PPCPs) in water and sediment samples obtained from Danjiangkou Reservoir during two seasonal sampling periods were studied to determine their impact on water quality. The temporal and spatial variations in concentrations measured were analyzed and related to ecological risks with data obtained during the mean-flow period (in June) and the dry period (in November). We found a high detection rate of ketoprofen (KTP) in water samples from Danjiangkou Reservoir; the concentrations ranged from not detected (ND) to 46.80ng/L with the highest values measured in the Hanku tributary samples followed by the samples collected in the main body of Danjiangkou Reservoir. The KTP concentrations in the Danku tributary samples were the lowest measured in this study. In addition, the concentrations of KTP in the Shending River, Sihe River, Jianghe River, Guanshan River, and Jianhe River water samples were relatively high in the mean-flow period. The water sample detection rates and concentrations of triclosan (TCS) and triclocarban (TCC) were low in both the mean-flow period and the dry period. All three kinds of PPCPs were detected in the sediment samples with the concentrations of KTP, TCS, and TCC ranging from 0.76 to 7.89μg/kg, 0.01 to 0.59μg/kg, and 0.01 to 11.36μg/kg, respectively. Overall, the concentrations of the three measured PPCPs in the water and sediment samples were all relatively low compared to results reported in the recent literature. The dry period concentrations of PPCPs in the water samples were lower than the concentrations measured in the mean-flow period. However, dry period concentrations were higher in the sediment samples compared to those in the mean-flow period samples. Our interpretation of the spatial and temporal patterns of PPCPs in Danjiangkou Reservoir suggests that these compounds were likely mainly derived from wastewater discharge in the upper reaches of the reservoir. The risk quotient (RQ) method was used for an ecological risk assessment of the detected PPCPs in this study. We found that TCS in water and sediment posed medium ecological risks to algae at different times of the year. In view of the extreme importance of water safety in Danjiangkou Reservoir, the ecological risks of PPCPs require additional attention.

Animal and human enteric viruses in water and sediment samples from dairy farms

The Meme River in Lokoja is a tributary of the River Niger and a place where household discharge their domestic and industrial refuse. This however makes the river to be highly polluted due to these discharges. This necessitates the present study to assess the level of heavy metals contamination in the coastal sediment of Meme River in Lokoja using Flame Atomic Absorption Spectrometric technique. The various levels of contamination was analysed using the geo-accumulation index. Results of this study for water analysis indicates a concentration range of 0.04 – 0.06 ppm (Fe), 2.33 – 10.40 ppm (Cr), 0.30 – 0.72 ppm (Zn), 0 – 1.81 ppm (Ni), 0.01 – 0.70 ppm (Cu) and 0.03 – 0.10 ppm (Cd). The observed metal concentrations for sediments ranged from 3.50 – 5.60 mg/kg (Fe), 5.93 – 9.89 mg/kg (Cr), 0.65 – 1.04 mg/kg (Zn), 0.13 – 2.45 mg/kg (Ni), 0.10 – 0.20 mg/kg (Cu) and 0.070 – 0.61 mg/kg (Cd). Results of some measured metals like K, Mg and Na in the water ranged from 30.0 – 44.0 ppm, 9.30 – 9.80 ppm, and 5.40 – 5.70 ppm respectively, while the concentration observed in the sediment samples ranged from 49.0 – 78.0 mg/kg (K), 9.50 – 9.80 mg/kg (Mg) and 5.55 – 5.68 mg/kg (Na). The geo-accumulation index analysis showed that the sediment and water samples are not polluted with Cr, Zn, Cu and Cd. However, the water samples are highly polluted with Fe. The measured metals such as Mg and K indicated a moderately high concentration in the water and sediment samples. The results of this work generally indicate that the sediment and water samples are moderately polluted by Fe which possibly may be due to anthropogenic activities along the River bank

Organophosphorus pollutants (OPP) in aquatic environment at Damietta Governorate, Egypt: Implications for monitoring and biomarker responses

Rivers are the natural drainage system, transporting anthropogenic wastes and pollution, including microplastics (plastic < 5 mm). In a riverine system, microplastics can enter from different sources, and have spatial variance in concentration, physical and chemical properties, and imposed risk to the ecosystem. This pilot study presents an examination of microplastics in water and sediment samples using a single sample collection from the rural Raquette River, NY to evaluate a hypothesis that distinct locations of the river, such as downstream of a wastewater treatment plant, upstream of a hydro-dam, and river confluence, may be locations of higher microplastics concentration. In general, our results revealed the presence of high microplastic concentrations downstream of the wastewater treatment plant (in sediments), upstream of the hydro dam (both water and sediment), and in the river confluence (water sample), compared to other study sites. Moreover, the risk assessment indicates that even in a rural river with most of its drainage basin comprising forested and agricultural land, water, and sediment samples at all three locations are polluted with microplastics (pollution load index, PLI > 1; PLIzone = 1.87 and 1.68 for water and sediment samples respectively), with risk categories between Levels I and IV (“minor” to “danger”). Overall, the river stands in a “considerable” risk category (PRIzone = 134 and 113 for water and sediment samples respectively). The overall objective of this pilot study was to evaluate our hypothesis and advance our understanding of microplastic dynamics in rural river systems, elucidating their introduction from a point source (wastewater treatment plant), transit through an impediment (hydro-dam), and release into a vital transboundary river (confluence of Raquette-St. Lawrence Rivers).

The diversity of Cyanobacteria in water and sediment samples from four representative sites of the Salar de Huasco was examined using denaturing gradient gel electrophoresis and analysis of clone libraries of 16S rRNA gene PCR products. Salar de Huasco is a high altitude (3800 m altitude) saline wetland located in the Chilean Altiplano. We analyzed samples from a tributary stream (H0) and three shallow lagoons (H1, H4, H6) that contrasted in their physicochemical conditions and associated biota. Seventy-eight phylotypes were identified in a total of 268 clonal sequences deriving from seven clone libraries of water and sediment samples. Oscillatoriales were frequently found in water samples from sites H0, H1 and H4 and in sediment samples from sites H1 and H4. Pleurocapsales were found only at site H0, while Chroococcales were recovered from sediment samples of sites H0 and H1, and from water samples of site H1. Nostocales were found in sediment samples from sites H1 and H4, and water samples from site H1 and were largely represented by sequences highly similar to Nodularia spumigena. We suggest that cyanobacterial communities from Salar de Huasco are unique - they include sequences related to others previously described from the Antarctic, along with others from diverse, but less extreme environments.

The current study aimed to investigate the total concentrations of heavy metals in water and sediment samples as well as their bioavailability in sediments of Musa Creek. Twenty samples including 10 sediments and 10 water samples were collected from 10 stations. The concentration of heavy metals was measured using inductively coupled plasma–mass spectrometry. The bioavailability of heavy metals was carried out by first step of Tessier sequential extraction method so called single extraction in the manuscript. The results showed that the mean concentrations of cadmium, chromium, nickel, and zinc in water samples was 0.17, 7.44, 43.80, and 8.85 µg/L, respectively. The concentration of lead was lower than the detection limit of the 0.1 µg/L. The positive correlation of heavy metals in water samples is due to their potential common source. The negative correlation of nickel with other elements in sediment samples indicates that, apart from the industrial activity in the region, the geogenic origin affects the concentration of metals. The factor analysis showed two components. The first component was lead, zinc, chromium, and cadmium with the common source (s) and nickel was the second component with geogenic origin. The high concentrations of heavy metals in the exchangeable phase of Tessier sequential extraction showed that the bioavailability of the elements in sediment samples, especially lead and zinc is at a high level that could be a serious threat to the aquatics of the region. Keywords: Heavy metals, Musa Creek, Bioavailability, Single extraction

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments.

Water and bed-sediment samples were collected by the U.S. Geological Survey (USGS) in 2009 and 2010 from 11 sites within California and 18 sites total in Colorado, Georgia, Idaho, Louisiana, Maine, and Oregon, and were analyzed for a suite of pesticides by the USGS. Water samples and bed-sediment samples were collected from perennial or seasonal ponds located in amphibian habitats in conjunction with research conducted by the USGS Amphibian Research and Monitoring Initiative and the USGS Toxic Substances Hydrology Program. Sites selected for this study in three of the states (California, Colorado, and Orgeon) have no direct pesticide application and are considered undeveloped and remote. Sites selected in Georgia, Idaho, Louisiana, and Maine were in close proximity to either agricultural or suburban areas. Water and sediment samples were collected once in 2009 during amphibian breeding seasons. In 2010, water samples were collected twice. The first sampling event coincided with the beginning of the frog breeding season for the species of interest, and the second event occurred 10-12 weeks later when pesticides were being applied to the surrounding areas. Additionally, water was collected during each sampling event to measure dissolved organic carbon, nutrients, and the fungus, Batrachochytrium dendrobatidis, which has been linked to amphibian declines worldwide. Bed-sediment samples were collected once during the beginning of the frog breeding season, when the amphibians are thought to be most at risk to pesticides. Results of this study are reported for the following two geographic scales: (1) for a national scale, by using data from the 29 sites that were sampled from seven states, and (2) for California, by using data from the 11 sampled sites in that state. Water samples were analyzed for 96 pesticides by using gas chromatography/mass spectrometry. A total of 24 pesticides were detected in one or more of the 54 water samples, including 7 fungicides, 10 herbicides, 4 insecticides, 1 synergist, and 2 pesticide degradates. On a national scale, aminomethylphosphonic acid (AMPA), the primary degradate of the herbicide glyphosate, which is the active ingredient in Roundup®, was the most frequently detected pesticide in water (16 of 54 samples) followed by glyphosate (8 of 54 samples). The maximum number of pesticides observed at a single site was nine compounds in a water sample from a site in Louisiana. The maximum concentration of a pesticide or degradate observed in water was 2,880 nanograms per liter of clomazone (a herbicide) at a site in Louisiana. In California, a total of eight pesticides were detected among all of the low and high elevation sites; AMPA was the most frequently detected pesticide, but glyphosate was detected at the highest concentrations (1.1 micrograms per liter). Bed-sediment samples were analyzed for 94 pesticides by using accelerated solvent extraction, gel permeation chromatography for sulfur removal, and carbon/alumina stacked solid-phase extraction cartridges to remove interfering sediment matrices. In bed sediment, 22 pesticides were detected in one or more of the samples, including 9 fungicides, 3 pyrethroid insecticides, p,p'-dichlorodiphenyltrichloroethane (p,p'-DDT) and its major degradates, as well as several herbicides. Pyraclostrobin, a strobilurin fungicide, and bifenthrin, a pyrethroid insecticide, were detected most frequently. Maximum pesticide concentrations ranged from less than their respective method detection limits to 1,380 micrograms per kilogram (tebuconazole in California). The number of pesticides detected in samples from each site ranged from zero to six compounds. The sites with the greatest number of pesticides were in Maine and Oregon with six pesticides detected in one sample from each state, followed by Georgia with four pesticides in one sample. For California, a total of 10 pesticides were detected among all sites, and 4 pesticides were detected at both low and high elevation sites; tebuconazole and pyraclostrobin were the two most frequently detected pesticides in California. For the other six selected states, the most frequently detected pesticides in bed sediment were pyraclostrobin (detected in 17 of 42 samples), bifenthrin (detected in 14 of 42 samples), and tebuconazole (detected in 10 of 42 samples). The fungus, Batrachochytrium dendrobatidis (Bd), was detected in water samples in sites from four of the seven states during 2009 and 2010, and the number of zoospore equivalents per liter of water in samples where Bd was detected ranged from 1.6 to 343. Bd was not detected in water samples from sites in Georgia, Louisiana, and Oregon.

Seasonal changes in organotin compounds in water and sediment samples from the semi-closed Port of Gdynia