High-quality treated wastewater causes remarkable changes in natural microbial communities and intI1 gene abundance

The demand for energy and chemicals is constantly growing, leading to an increase of the amounts of contaminants discharged to the environment. Among these, pharmaceutical molecules are frequently found in treated wastewater that is discharged into superficial waters. Indeed, wastewater treatment plants (WWTPs) are designed to remove organic pollution from urban effluents but are not specific, especially toward contaminants of emerging concern (CECs), which finally reach the natural environment. In this context, it is important to study the fate of micropollutants, especially in a soil aquifer treatment (SAT) context for water from WWTPs, and for the most persistent molecules such as benzodiazepines. In the present study, soils sampled in a reed bed frequently flooded by water from a WWTP were spiked with diazepam and oxazepam in microcosms, and their concentrations were monitored for 97 days. It appeared that the two molecules were completely degraded after 15 days of incubation. Samples were collected during the experiment in order to follow the dynamics of the microbial communities, based on 16S rRNA gene sequencing for Archaea and Bacteria, and ITS2 gene for Fungi. The evolution of diversity and of specific operating taxonomic units (OTUs) highlighted an impact of the addition of benzodiazepines, a rapid resilience of the fungal community and an evolution of the bacterial community. It appeared that OTUs from the Brevibacillus genus were more abundant at the beginning of the biodegradation process, for diazepam and oxazepam conditions. Additionally, Tax4Fun tool was applied to 16S rRNA gene sequencing data to infer on the evolution of specific metabolic functions during biodegradation. It finally appeared that the microbial community in soils frequently exposed to water from WWTP, potentially containing CECs such as diazepam and oxazepam, may be adapted to the degradation of persistent contaminants.

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Impact of treated wastewater for irrigation on soil microbial communities

The Science of The Total Environment ◽

10.1016/j.scitotenv.2017.10.039 ◽

2018 ◽

Vol 622-623 ◽

pp. 1603-1610 ◽

Cited By ~ 42

Author(s):

A.M. Ibekwe ◽

A. Gonzalez-Rubio ◽

D.L. Suarez

Keyword(s):

Microbial Communities ◽

Soil Microbial Communities ◽

Treated Wastewater ◽

Soil Microbial

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Agriculture, water and the environment: future challenges

Water Science & Technology Water Supply ◽

10.2166/ws.2003.0045 ◽

2003 ◽

Vol 3 (4) ◽

pp. 51-57 ◽

Cited By ~ 3

Author(s):

G. Oron

Keyword(s):

Supply And Demand ◽

Water Source ◽

Water Sources ◽

Additional Treatment ◽

Treated Wastewater ◽

Secondary Effluent ◽

Arid Zones ◽

Runoff Water ◽

High Quality ◽

Future Challenges

Various countries in the Mediterranean Basin and other arid and semi-arid regions are facing a gap between water supply and demand. This gap is closely linked with agricultural production and environmental issues. It is probably due to small amounts of precipitation and low availability of natural water sources. Special ventures have to be undertaken in order to supply water at adequate quality for all requirements. These can be accomplished by development of additional water sources that currently are considered marginal. The additional sources include saline ground water, treated wastewater and runoff water and are usually required to augment the limited supply from the regional conventional high quality local sources. The paper presented options for development of the marginal water sources in arid zones in conjunction with minimizing the dependence on high quality water. Domestic secondary effluent is a valuable water source for reclamation however, additional treatment is required to use it for unrestricted purposes. It can be achieved primarily by implementation of the membrane technology, namely ultrafiltration (UF) and reverse osmosis (RO) stages.

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Draft metagenomes of endolithic cyanobacteria and co-habitants from hyper-arid deserts

10.1101/2021.02.23.432541 ◽

2021 ◽

Author(s):

Bayleigh Murray ◽

Micah Dailey ◽

Emine Ertekin ◽

Jocelyne DiRuggiero

Keyword(s):

Microbial Communities ◽

Metabolic Pathways ◽

High Quality

AbstractCyanobacteria are essential to microbial communities inhabiting translucent rocks in hyper-arid deserts. Metagenomic studies revealed unique adaptations of these cyanobacteria but validation of the corresponding metabolic pathways remained challenging without access to isolates. Here we present high-quality metagenome assembled genomes for cyanobacteria, and their heterotrophic companions, isolated from endolithic substrates.

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MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

10.1101/2021.09.10.459728 ◽

2021 ◽

Author(s):

Vijini Mallawaarachchi ◽

Yu Lin

Keyword(s):

Microbial Communities ◽

De Novo ◽

State Of The Art ◽

Genetic Material ◽

Single Copy ◽

Experimental Results ◽

Marker Genes ◽

High Quality ◽

Second Best ◽

Direct Use

ABSTRACTMetagenomics binning has allowed us to study and characterize various genetic material of different species and gain insights into microbial communities. While existing binning tools bin metagenomics de novo assemblies, they do not make use of the assembly graphs that produce such assemblies. Here we propose MetaCoAG, a tool that utilizes assembly graphs with the composition and coverage information to bin metagenomic contigs. MetaCoAG uses single-copy marker genes to estimate the number of initial bins, assigns contigs into bins iteratively and adjusts the number of bins dynamically throughout the binning process. Experimental results on simulated and real datasets demonstrate that MetaCoAG significantly outperforms state-of-the-art binning tools, producing more high-quality bins than the second-best tool, with an average median F1-score of 88.40%. To the best of our knowledge, MetaCoAG is the first stand-alone binning tool to make direct use of the assembly graph information. MetaCoAG is available at https://github.com/Vini2/MetaCoAG.

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Microbial Community Stratification Linked to Utilization of Carbohydrates and Phosphorus Limitation in a Boreal Peatland at Marcell Experimental Forest, Minnesota, USA

Applied and Environmental Microbiology ◽

10.1128/aem.00205-14 ◽

2014 ◽

Vol 80 (11) ◽

pp. 3518-3530 ◽

Cited By ~ 61

Author(s):

Xueju Lin ◽

Malak M. Tfaily ◽

J. Megan Steinweg ◽

Patrick Chanton ◽

Kaitlin Esson ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Hot Spot ◽

Microbial Community Composition ◽

Phosphorus Limitation ◽

Rrna Gene ◽

Content Type ◽

Gene Abundance ◽

P Limitation

ABSTRACTThis study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance ofAcidobacteriaand theSyntrophobacteraceae, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance ofArchaea(primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by theMethanosarcinalesin the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at MEF, and microbial communities are structured by the dominant shrub,Chamaedaphne calyculata, which may act as a carbon source for major consumers in the peatland.

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Evaluating de novo assembly and binning strategies for time-series drinking water metagenomes.

10.1101/2021.07.11.451960 ◽

2021 ◽

Author(s):

Solize Vosloo ◽

Linxuan Huo ◽

Christopher L Anderson ◽

Maria Sevillano Rivera ◽

Zihan Dai ◽

...

Keyword(s):

Time Series ◽

Drinking Water ◽

Microbial Communities ◽

De Novo ◽

Sequence Data ◽

Data Mapping ◽

High Quality ◽

Systematic Assessment ◽

Medium Quality ◽

Crucial Part

Reconstructing microbial genomes from metagenomic short-read data can be challenging due to the unknown and uneven complexity of microbial communities. This complexity encompasses highly diverse populations which often includes strain variants. Reconstructing high-quality genomes is a crucial part of the metagenomic workflow as subsequent ecological and metabolic inferences depend on their accuracy, quality, and completeness. In contrast to microbial communities in other ecosystems, there has been no systematic assessment of genome-centric metagenomic workflows for drinking water microbiomes. In this study, we assessed the performance of a combination of assembly and binning strategies for time-series drinking water metagenomes that were collected over a period of 6 months. The goal of this study was to identify the combination of assembly and binning approaches that results in high quality and quantity metagenome-assembled genomes (MAGs), representing most of the sequenced metagenome. Our findings suggest that the metaSPAdes co-assembly strategies had the best performance as they resulted in larger and less fragmented assemblies with at least 85% of the sequence data mapping to contigs greater than 1kbp. Furthermore, a combination of metaSPAdes co-assembly strategies and MetaBAT2 produced the highest number of medium-quality MAGs while capturing at least 70% of the metagenomes based on read recruitment. Utilizing different assembly/binning approaches also assist in the reconstruction of unique MAGs from closely related species that would have otherwise collapsed into a single MAG using a single workflow. Overall, our study suggests that leveraging multiple binning approaches with different metaSPAdes co-assembly strategies may be required to maximize the recovery of good-quality MAGs, which more accurately capture the microbial diversity of drinking water samples.

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Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs

Applied and Environmental Microbiology ◽

10.1128/aem.03378-16 ◽

2017 ◽

Vol 83 (10) ◽

Cited By ~ 23

Author(s):

Christopher Staley ◽

Thomas Kaiser ◽

Maribeth L. Gidley ◽

Ian C. Enochs ◽

Paul R. Jones ◽

...

Keyword(s):

Next Generation Sequencing ◽

Coral Reefs ◽

Microbial Communities ◽

Treated Wastewater ◽

Coral Tissue ◽

Next Generation ◽

Sources Of Pollution ◽

Reef Communities ◽

Coastal Inlet ◽

Generation Sequencing

ABSTRACT Coral reefs are dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfalls of municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coral tissue samples (mucus and polyps) were characterized to determine the relationships between microbial communities in these matrices and those in reef water and coral tissues. Significant differences in microbial communities were noted among all sample types but varied between sampling areas. Contamination from outfalls was found to be the greatest potential source of LBSP influencing native microbial community structure among all reef samples, although pollution from inlets was also noted. Notably, reef water and coral tissue communities were found to be more greatly impacted by LBSP at southern reefs, which also experienced the most degradation during the course of the study. The results of this study provide new insights into how microbial communities from LBSP can impact coral reefs in southeast Florida and suggest that wastewater outfalls may have a greater influence on the microbial diversity and structure of these reef communities than do contaminants carried in runoff, although the influences of runoff and coastal inlet discharge on coral reefs are still substantial. IMPORTANCE Coral reefs are known to be endangered due to sewage discharge and to runoff of nutrients, pesticides, and other substances associated with anthropogenic activity. Here, we used next-generation sequencing to characterize the microbial communities of potential contaminant sources in order to determine how environmental discharges of microbiota and their genetic material may influence the microbiomes of coral reef communities and coastal receiving waters. Runoff delivered through inlet discharges impacted coral microbial communities, but impacts from oceanic outfalls carrying treated wastewater were greater. Geographic differences in the degree of impact suggest that coral microbiomes may be influenced by the microbiological quality of treated wastewater.

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Effect of irrigation with nutrient solutions mixed with treated wastewater on Asiatic lily ‘Brunello’ grown in a closed soilless culture

Acta agriculturae Slovenica ◽

10.14720/aas.2017.109.1.03 ◽

2017 ◽

Vol 109 (1) ◽

pp. 29

Author(s):

Ahmed Abdel-Nabi Al-Hammouri ◽

Khalid Al-Ghawanmeh ◽

Nabeel Bani Hani ◽

Nabeela Karam

Keyword(s):

Electrical Conductivity ◽

Nutrient Solution ◽

Dry Mass ◽

Treated Wastewater ◽

Soilless Culture ◽

Cut Flowers ◽

High Quality ◽

Greenhouse Study ◽

Potential Use ◽

Nutrient Solutions

A plastic greenhouse study was implemented to evaluate the potential use of treated wastewater for irrigation of Asiatic lily ‘Brunello’ grown in zeolite. Plants received the following treatments: a nutrient solution (N) alone, (N) mixed with treated wastewater (W) at rates of 3N:1W, 1N:1W and 1N:3W respectively. A closed system was used in which the drain solution was circulated for several days until its electrical conductivity reached 2.3 dS m-1, after which fresh irrigation solutions were used to start a second cycle of circulation. The results indicated that plants irrigated with (N) or 3N:1W solution had the longest stems (34.4 and 36.2 cm) respectively, peduncles and buds (about 4.5 cm), and the greatest shoot (3.4 and 3.8 cm) and bud mass (14.95 and 17.6 g) respectively. Plants irrigated with 1N:3W solution had the highest dry mass tissue content of K (3.06 g kg -1) and B (35.5 mg kg-1). Plants irrigated with 1N:1W or 1N:3W were inferior to other plants. It can be concluded that 1N:3W mixture may be used for production of high quality cut flowers of lily. Moreover, it is expected to save 3.4 litres m-2 of a nutrient solution and 1850, 347 and 1870 mg m-2 day-1 for N, P, and K respectively.

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