Advanced microbial analysis for wastewater quality monitoring: metagenomics trend

Is redox zonation an appropriate method for determining the stage of natural remediation in deep contaminated groundwater?

Groundwater contamination resulting from petroleum development poses a significant threat to drinking water sources, especially in developing countries. In situ natural remediation methods, including microbiological processes, have gained popularity for the reduction of groundwater contaminants. However, assessing the stage of remediation in deep contaminated groundwater is challenging and costly due to the complexity of diverse geological conditions and unknown initial concentrations of contaminants. This research proposes that redox zonation may be a more convenient and comprehensive indicator than the concentration of contaminants for determining the stage of natural remediation in deep groundwater. The combination of sequencing microbial composition using the high-throughput 16S rRNA gene and function predicted by FAPROTAX is a useful approach to determining the redox conditions of different contaminated groundwater. The sulfate-reducing environment, represented by Desulfobacteraceae, Peptococcaceae, Desulfovibrionaceae, and Desulfohalobiaceae could be used as characteristic early stages of remediation for produced water contamination in wells with high concentrations of SO42-, benzene, and salinity. The nitrate-reducing environment, enriched with microorganisms related to denitrification, sulfur-oxidizing, and methanophilic microorganisms could be indicative of the mid stages of in situ bioremediation. The oxygen reduction environment, enriched with oligotrophic and pathogenic Sphingomonadaceae, Caulobacteraceae, Syntrophaceae, Legionellales, Moraxellaceae, and Coxiellaceae, could be indicative of the late stages of remediation. This comprehensive approach could provide valuable insights into the process of natural remediation and facilitate improved environmental management in areas of deep contaminated groundwater.

Nanopore Sequencing Assessment of Bacterial Pathogens and Associated Antibiotic Resistance Genes in Environmental Samples

As seen in earlier and present pandemics, monitoring pathogens in the environment can offer multiple insights on their spread, evolution, and even future outbreaks. The present paper assesses the opportunity to detect microbial pathogens and associated antibiotic resistance genes, in relation to specific pathogen sources, by using nanopore sequencing in municipal waters and wastewaters in Romania. The main results indicated that waters collecting effluents from a meat processing facility exhibit altered communities' diversity and abundance, with reduced values (101-108 and 0.86-0.91) of Chao1 and, respectively, Simpson diversity indices and Campylobacterales as main order, compared with other types of municipal waters where the same diversity index had much higher values of 172-214 and 0.97-0.98, and Burkholderiaceae and Pseudomonadaceae were the most abundant families. Moreover, the incidence and type of antibiotic resistance genes were significantly influenced by the proximity of antibiotic sources, with either tetracycline (up to 45% of total reads) or neomycin, streptomycin and tobramycin (up to 3.8% total reads) resistance incidence being shaped by the sampling site. As such, nanopore sequencing proves to be an easy-to-use, accessible molecular technique for environmental pathogen surveillance and associated antibiotic resistance genes.

Roles and regulation of quorum sensing in anaerobic granular sludge: Research status, challenges, and perspectives

Anaerobic granular sludge (AnGS) has a complex and important internal microbial communication system due to its unique microbial layered structure. As a concentration-dependent communication system between bacterial cells through signal molecules, QS (quorum sensing) is widespread in AnGS and exhibits great potential to regulate microbial behaviors. Therefore, the universal functions of QS in AnGS have been systematically summarized in this paper, including the influence on the metabolic activity, physicochemical properties, and microbial community of AnGS. Subsequently, the common QS-based AnGS regulation approaches are reviewed and analyzed comprehensively. The regulation mechanism of QS in AnGS is analyzed from two systems of single bacterium and mixed bacteria. This review can provide a comprehensive understanding of QS functions in AnGS systems, and promote the practical application of QS-based strategies in optimization of AnGS treatment process.

High-throughput sequencing as a tool for monitoring prokaryote communities in a wastewater treatment plant

In this study, the DNA metabarcoding technique was used to explore the prokaryote diversity and community structure in wastewater collected in spring and winter 2020-2021 as well as the efficiency of the treatment in a wastewater treatment plant (WWTP) in Ría de Vigo (NW Spain). The samplings included raw wastewater from the inlet stream (M1), the discharge water after the disinfection treatment (M3) and mussels used as bioindicators of possible contamination of the marine environment. Significant differences were discovered in the microbiome of each type of sample (M1, M3 and mussels), with 92 %, 45 % and 44 % of exclusive OTUs found in mussel, M3 and M1 samples respectively. Seasonal differences were also detected in wastewater samples, with which abiotic parameters (temperature, pH) could be strongly involved. Bacteria present in raw wastewater (M1) were associated with the human gut microbiome, and therefore, potential pathogens that could be circulating in the population in specific periods were detected (e.g., Arcobacter sp. and Clostridium sp.). A considerable decrease in putative pathogenic organisms from the M1 to M3 wastewater fractions and the scarce presence in mussels (<0.5 % total reads) confirmed the effectiveness of pathogen removal in the wastewater treatment plant. Our results showed the potential of the DNA metabarcoding technique for monitoring studies and confirmed its application in wastewater-based epidemiology (WBE) and environmental contamination studies. Although this technique cannot determine if the infective pathogens are present, it can characterize the microbial communities and the putative pathogens that are circulating through the population (microbiome of M1) and also confirm the efficacy of depuration treatment, which can directly affect the aquaculture sector and even human and veterinary health.

Bioprospecting of microbial enzymes: current trends in industry and healthcare

Microbial enzymes have an indispensable role in producing foods, pharmaceuticals, and other commercial goods. Many novel enzymes have been reported from all domains of life, such as plants, microbes, and animals. Nonetheless, industrially desirable enzymes of microbial origin are limited. This review article discusses the classifications, applications, sources, and challenges of most demanded industrial enzymes such as pectinases, cellulase, lipase, and protease. In addition, the production of novel enzymes through protein engineering technologies such as directed evolution, rational, and de novo design, for the improvement of existing industrial enzymes is also explored. We have also explored the role of metagenomics, nanotechnology, OMICs, and machine learning approaches in the bioprospecting of novel enzymes. Overall, this review covers the basics of biocatalysts in industrial and healthcare applications and provides an overview of existing microbial enzyme optimization tools. KEY POINTS: • Microbial bioactive molecules are vital for therapeutic and industrial applications. • High-throughput OMIC is the most proficient approach for novel enzyme discovery. • Comprehensive databases and efficient machine learning models are the need of the hour to fast forward de novo enzyme design and discovery.

Rethinking water treatment targets: Bacteria regrowth under unprovable conditions

Ozonation is among the currently used technologies to remove chemical and biological contaminants from secondary treated urban wastewater (UWW). Despite its effectiveness on the abatement of organic micropollutants (OMPs) and disinfection, previous studies have shown that regrow of bacteria may occur upon storage of the ozonated UWW. This reactivation has been attributed to the high content of assimilable organic carbon after treatment. In order to investigate if ozonation by-products are the main biological regrowth drivers in stored ozonated UWW, the ozonation surviving cells were resuspended in sterile bottled mineral water (MW), simulating a pristine oligotrophic environment. After 7 days storage, organisms such as Acinetobacter, Methylobacterium, Cupriavidus, Massilia, Acidovorax and Pseudomonas were dominant in both ozonated UWW and pristine MW, demonstrating that bacterial regrowth is not strictly related to the eventual presence of ozonation by-products, but instead with the ability of the surviving cells to cope with nutrient-poor environments. The resistome of UWW before and after ozonation was analysed by metagenomic techniques. Draft metagenome assembled genomes (dMAGs), recovered from both ozonated UWW and after cell resuspension in MW, harboured genes conferring resistance to diverse antibiotics classes. Some of these antibiotic resistance genes (ARGs) were located in the vicinity of mobile genetic elements, suggesting their potential to be mobilized. Among these, dMAGs affiliated to taxa with high relative abundance in stored water, such as P. aeruginosa and Acinetobacter spp., harboured ARGs conferring resistance to 12 and 4 families of antibiotics, respectively, including those encoding carbapenem hydrolysing oxacillinases. The results herein obtained point out that the design and development of new wastewater treatment technologies should include measures to attenuate the imbalance of the bacterial communities promoted by storage of the final treated wastewater, even when applying processes with high mineralization rates.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health

Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.

Scientometric analysis of the term 'microbiota' in research publications (1999-2017): a second youth of a century-old concept

Great progress in microbiota research during last decades resulted in a growing corpus of publications mentioning the term 'microbiota'. Specifically, the human microbiota increasingly recognised nowadays as one of the most important health challenges is becoming an emerging research front. By examining over 28 000 microbiota-related papers from the Web of Science database, our study aims to characterise the evolution of publication patterns in this field between 1999 and 2017. The corpus is first analysed in terms of breakdown by journal subject categories, then an additional insight in the structuring of the microbiota research into different topics is provided by means of topic modelling. Our results demonstrate that over time (i) a substantial increase in the publications number is accompanied by a broad diversification of associated journal subject categories; (ii) the research focus moved outside from its primary research field showing successive shifts from dentistry and ecologically centred areas, through agri-food applied topics, towards the most recent clinical applications. The trends in thematic structure of the field presented from a historical perspective suggest that the current systemic approach to host-microbiota relationship inherited from the ecological background of the concept of microbiota has opened up a number of new research directions and perspectives.

Metagenomic insights into microbial characterizations in explaining the distinction of biofilter performance during start-up

As an effective alternative for dissolved nitrogen removal, biofilter closely associates its treatment performance to structural and/or operational conditions. In this study, a set of four different biofilters including MAVF (mature aerated vertical flow), NAVF (new aerated vertical flow), NVF (new non-aerated vertical flow), and BHF (baffled non-aerated horizontal flow) were employed to purify low C/N ratio (3.8) domestic wastewater. All the filters were packed with round ceramsite operated under varying hydraulic loading rates (HLRs) of 0.024-0.18 m/day. During the start-up, both the physicochemical and microbial characterizations were investigated. It was found that, carbon and nitrogen could achieve ideal removal in MAVF once added with further sedimentation, while phosphorus displayed an unsatisfactory sequestration in any of the four filters probably due to the high inflow load and/or lack of alternate anaerobic/aerobic conditions. Filter clustering based on percent removal and removal rate constant displayed a consistent pattern, which was similar to that based on taxa of phylum from 16S rRNA sequencing, or phylum/genus/species from shotgun metagenomic sequencing although there were obvious distinctions in taxa compositions among direct comparison. Meanwhile, gene function annotation revealed that filter clustering based on metabolic pathways was consistent with that based on purification performance. These consistencies might imply that the treatment performance was mainly determined by microbial degradation. The enrichment of specific functional microbes responsible for the degradation of certain pollutants, such as carbohydrates, matched well with the defined purification performance.

Identification of eukaryotic microorganisms with 18S rRNA next-generation sequencing in wastewater treatment plants, with a more targeted NGS approach required for Cryptosporidium detection

While some microbial eukaryotes can improve effluent quality in wastewater treatment plants (WWTPs), eukaryotic waterborne pathogens are a threat to public health. This study aimed to identify Eukarya, particularly faecal pathogens including Cryptosporidium, in different treatment stages (influent, intermediate and effluent) from four WWTPs in Western Australia (WA). Three WWTPs that utilise stabilisation ponds and one WWTP that uses activated sludge (oxidation ditch) treatment technologies were sampled. Eukaryotic 18S rRNA (18S) was targeted in the wastewater samples (n = 26) for next-generation sequencing (NGS), and a mammalian-blocking primer was used to reduce the amplification of mammalian DNA. Overall, bioinformatics analyses revealed 49 eukaryotic phyla in WWTP samples, and three of these phyla contained human intestinal parasites, which were primarily detected in the influent. These human intestinal parasites either had a low percent sequence composition or were not detected in the intermediate and effluent stages and included the amoebozoans Endolimax sp., Entamoeba sp. and Iodamoeba sp., the human pinworm Enterobius vermicularis (Nematoda), and Blastocystis sp. subtypes (Sarcomastigophora). Six Blastocystis subtypes and four Entamoeba species were identified by eukaryotic 18S NGS, however, Cryptosporidium sp. and Giardia sp. were not detected. Real-time polymerase chain reaction (PCR) also failed to detect Giardia, but Cryptosporidium-specific NGS detected Cryptosporidium in all WWTPs, and a total of nine species were identified, including five zoonotic pathogens. Although eukaryotic 18S NGS was able to identify some faecal pathogens, this study has demonstrated that more specific NGS approaches for pathogen detection are more sensitive and should be applied to future wastewater pathogen assessments.

Evaluation of 16S next-generation sequencing of hypervariable region 4 in wastewater samples: An unsuitable approach for bacterial enteric pathogen identification

Recycled wastewater can carry human-infectious microbial pathogens and therefore wastewater treatment strategies must effectively eliminate pathogens before recycled wastewater is used to supplement drinking and agricultural water supplies. This study characterised the bacterial composition of four wastewater treatment plants (WWTPs) (three waste stabilisation ponds and one oxidation ditch WWTP using activated sludge treatment) in Western Australia. The hypervariable region 4 (V4) of the bacterial 16S rRNA (16S) gene was sequenced using next-generation sequencing (NGS) on the Illumina MiSeq platform. Sequences were pre-processed in USEARCH v10.0 and denoised into zero-radius taxonomic units (ZOTUs) with UNOISE3. Taxonomy was assigned to the ZOTUs using QIIME 2 and the Greengenes database and cross-checked with the NCBI nr/nt database. Bacterial composition of all WWTPs and treatment stages (influent, intermediate and effluent) were dominated by Proteobacteria (29.0-87.4%), particularly Betaproteobacteria (9.0-53.5%) and Gammaproteobacteria (8.6-34.6%). Nitrifying bacteria (Nitrospira spp.) were found only in the intermediate and effluent of the oxidation ditch WWTP, and denitrifying and floc-forming bacteria were detected in all WWTPs, particularly from the families Comamonadaceae and Rhodocyclales. Twelve pathogens were assigned taxonomy by the Greengenes database, but comparison of sequences from genera and families known to contain pathogens to the NCBI nr/nt database showed that only three pathogens (Arcobacter venerupis, Laribacter hongkongensis and Neisseria canis) could be identified in the dataset at the V4 region. Importantly, Enterobacteriaceae genera could not be differentiated. Family level taxa assigned by Greengenes database agreed with NCBI nr/nt in most cases, however, BLAST analyses revealed erroneous taxa in Greengenes database. This study highlights the importance of validating taxonomy of NGS sequences with databases such as NCBI nr/nt, and recommends including the V3 region of 16S in future short amplicon NGS studies that aim to identify bacterial enteric pathogens, as this will improve taxonomic resolution of most, but not all, Enterobacteriaceae species.

Biosensors-Publication Trends and Knowledge Domain Visualization

The number of scholarly publications on the topic of biosensors has increased rapidly; as a result, it is no longer easy to build an informed overview of the developments solely by manual means. Furthermore, with many new research results being continually published, it is useful to form an up-to-date understanding of the recent trends or emergent directions in the field. This paper utilizes bibliometric methods to provide an overview of the developments in the topic based on scholarly publications. The results indicate an increasing interest in the topic of biosensor(s) with newly emerging sub-topics. The US is identified as the country with highest total contribution to this area, but as a collective, EU countries top the list of total contributions. An examination of trends over the years indicates that in recent years, China-based authors have been more productive in this area. If research contribution per capita is considered, Singapore takes the top position, followed by Sweden, Switzerland and Denmark. While the number of publications on biosensors seems to have declined in recent years in the PubMed database, this is not the case in the Web of Science database. However, there remains an indication that the rate of growth in the more recent years is slowing. This paper also presents a comparison of the developments in publications on biosensors with the full set of publications in two of the main journals in the field. In more recent publications, synthetic biology, smartphone, fluorescent biosensor, and point-of-care testing are among the terms that have received more attention. The study also identifies the top authors and journals in the field, and concludes with a summary and suggestions for follow up research.