Occurrences and implications of pathogenic and antibiotic-resistant bacteria in different stages of drinking water treatment plants and distribution systems.

Different stages of drinking water treatment plants (DWTPs) play specific roles in diverse contaminants' removal present in natural water sources. Although the stages are recorded to promote adequate treatment of water, the occurrence of pathogenic bacteria (PB) and antibiotic-resistant bacteria (ARB) in the treated water and the changes in their diversity and abundance as it passed down to the end users through the drinking water distribution systems (DWDSs), is a great concern, especially to human health. This could imply that the different stages and the distribution system provide a good microenvironment for their growth. Hence, it becomes pertinent to constantly monitor and document the diversity of PB and ARB present at each stage of the treatment and distribution system. This review aimed at documenting the occurrence of PB and ARB at different stages of treatment and distribution systems as well as the implication of their occurrence globally. An exhaustive literature search from Web of Science, Science-Direct database, Google Scholar, Academic Research Databases like the National Center for Biotechnology Information, Scopus, and SpringerLink was done. The obtained information showed that the different treatment stages and distribution systems influence the PB and ARB that proliferate. To minimize the human health risks associated with the occurrence of these PB, the present review, suggests the development of advanced technologies that can promote quick monitoring of PB/ARB at each treatment stage and distribution system as well as reduction of the cost of environomics analysis to promote better microbial analysis.

Characterization of the physicochemical composition of anaerobically digested (digestate) high throughput red meat abattoir waste in South Africa and the determination of its quality as a potential biofertilizer.

Anaerobic digestion as a treatment option for waste produced in high throughput red meat abattoirs in South Africa is now gaining interest in both private and government sectors. The resultant digested slurry (digestate) is currently being regarded as waste despite its nutritional value for soil and plants which can be harnessed if digestate is utilized as biofertilizer to ensure nutrient cycling. The study investigated the physicochemical and microbial characteristics of digestate emanating from anaerobic digestion of red meat abattoir waste in South Africa, as well as evaluating its potential use as biofertilizer. The pH, total solids, volatile solids, chemical oxygen demand, electrical conductivity, total volatile fatty acids and chemical composition were determined using standard methods. Microbial analyses were determined according to the serial dilution method (101- 1010). The results were benchmarked with Public Available Specifications (PAS) 110 standards for quality control of digestate intended to be used as biofertilizer for agricultural purposes. Results for pH, total solids, electrical conductivity, chemical oxygen demand, and total volatile fatty acids fell within the required PAS110 standard which requires standard limits of 6.5-9, 30 %-50 %, <1500 mg/L, <3000 µS/cm, and 0.43 COD/g VS respectively. Moisture content in all red meat abattoir digestate ranged from 92.05 ± 0.5 % to 95.49 ± 0.38 % and did not meet the required limit of <35 %. E. coli in untreated cattle and pig abattoir digestate were 1023 ± 35 cfu/mL and 1068 ± 51 cfu/mL, respectively, and also did not meet the required standard limit of <1000 cfu/mL. Chemical composition showed that abattoir digestate was abundant in both macronutrients and micronutrients, and heavy metal concentrations in all digestate samples fell within the PAS 110. In conclusion, abattoir digestate was observed to be highly abundant in nutrients essential for soil health and plant growth, and mostly met the required EU PAS110 standard for utilization as biofertilizer in agricultural land.

Multivariate analysis of enriched landfill soil consortia provide insight on the community structural perturbation and functioning during low-density polyethylene degradation.

Plastic-enriched sites like landfills have immense potential for discovery of microbial consortia that can efficiently degrade plastics. In this study, we used a combination of culture enrichment, high-throughput PacBio sequencing of 16 S rRNA and the ITS gene, Fourier transform infrared (FTIR), and scanning electron microscopy (SEM) to examine the compositional and diversity perturbations of bacterial and fungal consortia from landfill soils and their impact on low-density polyethylene (LDPE) film biodegradation over a 90-day period. Results showed that enrichment cultures effectively utilized LDPE as a carbon source for cellular growth, resulting in significant weight reduction (22.4% and 55.6%) in the films. SEM analysis revealed marked changes in the micrometric surface characteristics (cracks, fissures, and erosion) and biofilm formation in LDPE films. FTIR analyses suggested structural and functional group modification related to C-H (2831-2943 cm⁻¹), and CH2 (1400 cm⁻¹) stretching, CO and CC (680-950 cm⁻¹) scission, and CO incorporation (3320-3500 cm⁻¹) into the carbon backbone, indicative of LDPE polymer biodegradation. Enrichment cultures had lower diversity and richness of microbial taxa compared to soil samples, with LDPE as a carbon source having a direct influence on the structure and functioning of the microbial consortia. A total of 26 bacterial and 12 fungal OTU exhibiting high relative abundance and significant associations (IndVal > 0.7, q < 0.05) were identified in the enrichment culture. Bacterial taxa such as unclassified Parvibaculum FJ375498, Achromobacter xylosoxidans, unclassified Chitinophagaceae PAC002331, unclassified Paludisphaera and unclassified Comamonas JX898122, and six fungal species (Galactomyces candidus, Trichosporon chiropterorum, Aspergillus fumigatus, Penicillium chalabudae, Talaromyces thailandensis, and Penicillium citreosulfuratum) were identified as the putative LDPE degraders in the enrichment microbial consortium cultures. PICRUSt2 metagenomic functional profiling of taxonomic bacterial taxa abundances in both landfill soil and enrichment microbial consortia also revealed differential enrichment of energy production, stress tolerance, surface attachment and motility pathways, and xenobiotic degrading enzymes important for biofilm formation and hydrolytic/oxidative LDPE biodegradation. The findings shed light on the composition and structural changes in landfill soil microbial consortia during enrichment with LDPE as a carbon source and suggest novel LDPE-degrading bacterial and fungal taxa that could be explored for management of polyethylene pollution.

Fellowship of the Spring: An initiative to document and protect the world's oases.

An 'oasis' signifies a refugium of safety, recovery, relaxation, fertility, and productivity in an inhospitable desert, a sweet spot in a barren landscape where life-giving water spills forth from the Earth. Remarkable mythological congruencies exist across dryland cultures worldwide where oases or 'arid-land springs' occur. In many places they also provide specialised habitats for an extraordinary array of endemic organisms. To inform their management, and maintain their integrity, it is essential to understand the hydrogeology of aquifers and springs. Gravity-fed vs artesian aquifers; actively recharged vs fossil aquifers, and sources of geothermal activity are important concepts presented here. There consequences for oases of sustainable and unsustainable groundwater extraction, and other examples of effective conservation management. Oases are archetypes for human consciousness, habitats that deserve protection and conservation, and a lingua franca for multicultural values and scientific exchange. We represent an international Fellowship of the Spring seeking to encompass and facilitate the stewardship of oases and aquifers through improved knowledge, outreach, and governance.

The plastic and microplastic waste menace and bacterial biodegradation for sustainable environmental clean-up a review.

Environment plastic litter accumulation is a significant concern, needing urgent advancements in plastic waste management. Recent investigations into plastic biodegradation by bacteria and their enzymes are creating exciting unique opportunities for the development of biotechnological plastic waste treatment methods. This review summarizes information on bacterial and enzymatic biodegradation of plastic in a wide range of synthetic plastics such as polyethylene terephthalate (PET), polyethylene (PE), polypropylene (PP), polystyrene (PS), polyurethane (PUR), polytetrafluoroethylene (PTFE) and polyvinyl chloride (PVC). Plastic biodegradation is facilitated by Acinetobacter, Bacillus, Brevibacillus, Escherichia, Pseudomonas, Micrococcus, Streptomyces, and Rhodococcus bacteria, and enzymes such as proteases, esterases, lipases, and glycosidases. Molecular and analytical procedures used to analyze biodegradation processes are outlined, as are the obstacles in verifying plastic breakdown using these methods. Taken together, the findings of this study will contribute significantly to the construction of a library of high-efficiency bacterial isolates and consortiums and their enzymes for use in plastic biosynthesis. This information is useful to researchers investigating plastic bioremediation and a supplement to the scientific and grey literature already accessible. Finally, the review focuses on expanding the understanding of bacterial capacity to break-down plastic utilizing modern biotechnological methods, bio-nanotechnological-based materials, and their future role in resolving pollution problems.

Bioaugmentation potential of inoculum derived from anaerobic digestion feedstock for enhanced methane production using water hyacinth.

The utilisation of water hyacinth for production of biogas is considered to be a solution to both its control and the global renewable energy challenge. In this instance, an investigation was conducted to evaluate the potential of water hyacinth inoculum to enhance methane production during anaerobic digestion (AD). Chopped whole water hyacinth (10% (w/v)) was digested to prepare an inoculum consisting mainly of water hyacinth indigenous microbes. The inoculum was incorporated in the AD of freshly chopped whole water hyacinth to set up different ratios of water hyacinth inoculum and water hyacinth mixture with appropriate controls. The results of batch tests with water hyacinth inoculum showed a maximal cumulative volume of 211.67 ml of methane after 29 days of AD as opposed to 88.6 ml of methane generated from the control treatment without inoculum. In addition to improving methane production, inclusion of water hyacinth inoculum reduced the electrical conductivity (EC) values of the resultant digestate, and, amplification of nifH and phoD genes in the digestate accentuates it as a potential soil ameliorant. This study provides an insight into the potential of water hyacinth inoculum to enhance methane production and contribute to the feasibility of the digestate as a soil fertility enhancer.

Assessing the impact of COVID-19 restrictions on the microbial quality of an urban water catchment and the associated probability of waterborne infections.

The World Health Organization reported that COVID-19 cases reached 611,421,786 globally by September 23, 2022. Six months after the first reported case, the disease had spread rapidly, reaching pandemic status, leading to numerous preventive measures to curb the spread, including a complete shutdown of many activities worldwide. Such restrictions affected services like waste management, resulting in waste accumulation in many communities and increased water pollution. Therefore, the current study investigated if lockdown impacted surface water microbial quality within an urban water catchment in South Africa. Using quantitative microbial risk assessment, the study further assessed changes in the probability of infection (Pi) with gastrointestinal illnesses from exposure to polluted water in the catchment. Escherichia coli data for 2019, 2020 and 2021 - pre-COVID, lockdown, and post-lockdown periods, respectively - were collected from the area's wastewater treatment management authorities. The Pi was determined using a beta-Poisson model. Mean overall E. coli counts ranged from 2.93 ± 0.16 to 5.30 ± 1.07 Log10 MPN/100 mL. There was an overall statistically significant increase in microbial counts from 2019 to 2021. However, this difference was only accounted for between 2019 and 2021 (p = 0.008); the increase was insignificant between 2019 and 2020, and 2020 and 2021. The Pi revealed a similar trend for incidental ingestion of 100 mL and 1 mL of polluted water. No statistically significant difference was observed between the years based on multiple exposures. Although the overall microbial load and Pi estimated within the catchment exceeded the local and international limits recommended for safe use by humans, especially for drinking and recreation, these were not significantly affected by the COVID-19 restrictions. Nevertheless, these could still represent a health hazard to immunocompromised individuals using such water for personal and household hygiene, especially in informal settlements without access to water and sanitation services.

Contribution of pollution gradient to the sediment microbiome and potential pathogens in urban streams draining into Lake Victoria (Kenya).

In sub-Saharan Africa (SSA), urban rivers/streams have long been subjected to anthropogenic pollution caused by urbanization, resulting in significantly altered chemical and biological properties of surface water and sediments. However, little is known about the diversity and structure of river microbial community composition and pathogens, as well as how they respond to anthropogenic inputs. High-throughput 16S rRNA amplicon sequencing and PICRUSt predictive function profiling were used in this study to conduct a comprehensive analysis of the spatial bacterial distribution and metabolic functions in sediment of two urban streams (Kisat and Auji) flowing through Kisumu City, Kenya. Results revealed that sediment samples from the highly urbanized mid and lower stream catchment zones of both streams had significantly higher levels of total organic carbon (TOC), total nitrogen (TN), total phosphorous (TP) than the less urbanized upper catchment zone, and were severely polluted with toxic heavy metals lead (Pb), cadmium (Cd), and copper (Cu). Differential distribution of Actinobacteria, Proteobacteria, Chloroflexi, and Verrucomicrobia in sediment bacterial composition was detected along stream catchment zones. The polluted mid and lower catchment zones were rich in Actinobacteria and Proteobacteria, as well as a variety of potential pathogenic taxa such as Corynebacterium, Staphylococcus, Cutibacterium, Turicella, Acinetobacter, and Micrococcus, as well as enteric bacteria such as Faecalibacterium, Shewanella, Escherichia, Klebsiella, Enterococcus, Prevotella, Legionella, Vibrio and Salmonella. Furthermore, PICRUSt metabolic inference analysis revealed an increasing enrichment in the sediments of genes associated with carbon and nitrogen metabolism, disease pathogenesis, and virulence. Environmental factors (TOC, Pb, Cd, TN, pH) and geographical distance as significant drivers of sediment bacterial community assembly, with the environmental selection to play a dominant role. In polluted river catchment zone sediment samples, Pb content was the most influential sediment property, followed by TOC and Cd content. Given the predicted increase in urbanization in SSA, further alteration of surface water and sediment microbiome due to urban river pollution is unavoidable, with potential long-term effects on ecosystem function and potential health hazards. As a result, this study provides valuable information for ecological risk assessment and management of urban rivers impacted by diffuse and point source anthropogenic inputs, which is critical for future proactive and sustainable urban waste management, monitoring, and water pollution control in low-income countries.

Toxicity assessment of TiO2-conjugated Carbon-based nanohybrid material on a freshwater bioindicator cladoceran, Daphnia magna.

The application of nanocomposite materials fabricated from titanium dioxide nanoparticles (TiO2 NPs) and different carbon (C) allotropes have gained popularity in water treatment applications due to their synergistic properties. Studies to date have focused on simple forms of nanomaterials (NMs), however, with the technology development, there is a dramatic increase in production and application of these complex NMs which could result in toxicological impacts on organisms when released into aquatic environments. This raises serious concerns about their safety and the need to ascertain their potential adverse effects on aquatic organisms. While conjugated TiO2 NPs/carbon-based nanohybrids (TiO2/C-NHs) may exhibit enhanced photocatalytic activity, there is no research in the scientific community regarding their toxicological effects on D. magna, which are indicators of freshwater pollution. In this study, two under-represented TiO2/C-NHs (i.e., TiO2- conjugated carbon nanofiber (CNF), and TiO2-conjugated multi-walled carbon nanotube (CNT)) were investigated for their toxic effects on D. magna, through a series of acute toxicity tests with a set of sublethal biochemical biomarkers of oxidative stress. The lethal toxicity and oxidative stress formation of TiO2/C-NHs over 48 h revealed a concentration-dependant increase in D. magna mortality. The primary mechanism identified was the generation of ROS, which was in line with toxicity results. Light microscopy and CytoViva® images visualized D. magna interaction with the NPs, which accumulated and appeared as dark materials in the lines of the gut tract. The collective results indicate that TiO2/C-NHs have the potential to cause an effect on freshwater organisms when released into the environment. However, the relevance of TiO2/C-NHs effects needs further chronic toxicity studies since they show promise to be used in nano-bioremediation materials to treat wastewaters.

Effective treatment of acid mine drainage using a combination of MgO-nanoparticles and a series of constructed wetlands planted with Vetiveria zizanioides: A hybrid and stepwise approach.

In this novel study, acid mine drainage (AMD) was treated using a hybrid approach comprising a nano-and-biotic system synergistically integrated in a step-wise and modular fashion. Specifically, the treatment chains were made up of different stages, which comprise, neutralization using activated magnesite or MgO-nanoparticles (NPs) (Stage 1) and polishing the product water using a series of wetlands (Stage 2) in a step-wise connection. In stage One (1), real AMD was treated with MgO-NPs at a ratio of 1:100 (1 g/100 mL - w/v ratio), 500 rpm of mixing speed, and One (1) hour of hydraulic retention time (HRT) whilst in stage 2, the final water was fed into constructed wetlands, i.e. Three (3) interconnected wetland with different flow modalities [(I) subsurface vertical flow (SSVF-CW), (II) free water surface flow (FWS-CW), and (III) subsurface horizontal flow (SSHF-CW)], for further purification and polishing to the desired product. In this stage, i.e. stage 2, the product water and substrate were collected daily at the outlet and bottom of each wetland. After the treatment process, the pH of the product water was observed to have increased from 2.6 to 10.4. Significant removal of inorganic contaminants was also observed and the following removal sequence was registered, Fe (99.8%) ≥ Al (99.5%) ≥ Mn (99.24%) ≥ Zn (98.36%) ≥ Cu (97.38%) ≥ Ni (97.7%) ≥ SO42─ (80.59%). Reduction in electrical conductivity (EC) was also observed (86%). Specifically, the nano-part removed the metals and sulphate partially whereas the bio-part effectively removed SO42─ and EC levels, thus denoting stellar combination and complementary performance for the hybrid system in integrated fashion. The state-of-the-art analytical instruments were used to underpin and succinct the fate of chemical species in raw and product MgO-NPs, substrates, and the grass. Finally, the product water conformed to the prescribed standards for effluent discharge hence proving that the synergy of neutralization and bio-remediation, i.e. nano-and-biotic system, could potentially yield the desired results in mine water management and afield. This will go a long way in curtailing ecological footprints associated with mining activities thus fostering the concept of sustainable development.

Phytoremediation of soils contaminated by lead and cadmium in Ethiopia, using Endod (Phytolacca dodecandra L).

Phytoremediation is a cost effective and environmentally sustainable green technology for remediation of metal contaminated sites. In Addis Ababa, the capital of Ethiopia, large vegetable farms are grown on contaminated sites. This study evaluates the potential of Phytolacca dodecandra L to remediate Pb and Cd from contaminated sites in Addis Ababa. Pb and Cd in soil samples and different plant parts were determined using AAS. Phytoremediation potential of P. dodecandra in different seasons was estimated by calculating the Bioconcentration factor (BCF) and translocation factor (TF). The average BCF recorded for plant shoot in dry season samples varied from 0.87 to 1.74 for Pb and 1.06 to 2.00 for Cd, while in wet season it was within the range of 1.1-1.53 for Pb and 0.93-3.89 for Cd. The TF values for P. dodecandra ranged from 0.84 to 3.49 for Pb and 1.81 to 4.11 for Cd in dry season, whereas for wet season it varied between 1.34 and 2.01 for Pb and 1.78 and 2.97 for Cd. Since the mean values of BCF and TF were >1, it was concluded that P. dodecandra has considerable potential for phytoextraction of Pb and Cd in contaminated sites.

Toxicity evaluation of TiO2/MWCNT-CNF hybrid nanocomposites with enhanced photocatalytic activity toward freshwater microalgae: Pseudokirchneriella subcapitata.

A wide range of semiconductor-assisted photocatalytic nanomaterials (NMs) are currently being considered and investigated as potential photocatalysts in water treatment. The applications of nanocomposites composed of nano-structured titania (nano-TiO2) and multi-walled carbon nanotubes (MWCNTs) nanocomposites is growing markedly on account of enhanced photocatalytic efficiency. However, concurrent with the increasing production and application comes a serious concern of these emerging nanosystems about their potential risks in aquatic systems, and thereby potentially threatening aquatic organisms via toxic mechanisms that are, at present, poorly understood. In the present study, the lethal toxic effect and oxidative stress induced by TiO2/MWCNT-CNF nanocomposite in freshwater Pseudokirchneriella subcapitata were assessed. The growth inhibition and sublethal oxidative stress produced by the nanocomposites were evaluated on green microalgae P. subcapitata after 3 days of exposure at 24 h intervals. Moreover, the nanocomposites were physicochemically characterized using a combination of analytical techniques (XRD, SEM/EDS, HRTEM, TGA, UV-Visible spectroscopy). Evaluation of the hybrid for the photocatalytic degradation of Acid Violet 7 dye indicated an enhanced dye removal performance for TiO2/MWCNT-CNF (96.2%) compared to TiO2 (75.2%) after 2 h of visible light irradiation. While the nanocomposite showed good potential for the degradation of the azo dye, overall, the findings herein indicated that acute exposure of P. subcapitata to various concentrations of TiO2/MWCNT-CNF nanocomposite may cause algal growth inhibition including undesirable sublethal oxidative stress effects. The findings of this study contribute to a better understanding of the potential hazards of the developing nanocomposites materials towards the nano-bioremediation materials to treat wastewaters.

Correlations Between Root Metabolomics and Bacterial Community Structures in the Phragmites australis Under Acid Mine Drainage-Polluted Wetland Ecosystem.

Despite root microecology playing critical role in plant growth and fidelity, relatively few studies have focused on the link between the microbial communities and root metabolome in the aquatic macrophytes under heavy metal (HM) pollution. Using high-throughput metagenomic sequencing, targeted metabolomics and community-level physiological profile analyses, we investigated the symbiotic associations between Phragmites australis with rhizospheric bacterial communities under differing acid mine drainage (AMD) pollution. Results indicated that AMD pollution and root localization significantly affected root metabolome profiles. Higher accumulation of adenosine monophosphate, inosine, methionine, carnitine and dimethylglycine were observed in the rhizosphere under AMD than non-AMD habitat. Overall, the bacterial diversity and richness, and functional (metabolic) diversity were lower under high-AMD pollution. While non-AMD site was enriched with members of phylum Firmicutes, Proteobacteria were the most abundant taxa in the rhizosphere and endosphere under AMD-polluted sites. Further, plant growth promoting rhizobacteria (Rhizobium, Delftia, Bradyrhizobium, and Mesorhizobium) and metal-tolerant bacteria (Bacillus, Arthrobacter, Massilia and Methylocystis) were most abundant in AMD-polluted than non-AMD habitat. Finally, pH, TDS (total dissolved solids), Cu, Cr, Fe, and Zn content were the key environmental factors that strongly contributed to the spatial perturbation of rhizospheric metabolites, proteobacterial and acidobacterial taxa. Overall, the study linked the differential endospheric and rhizospheric bacterial community and metabolite profiles in P. australis under AMD environment and provided insights into HM adaptability and phytoremediation potential.

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi.

Identifying and adopting industrial applications for proteins and enzymes derived from fungi strains have been at the focal point of several studies in recent times. To facilitate such studies, it is necessary that advancements and innovation in mycological and molecular characterisation are concomitant. This review aims to provide a detailed overview of the necessary steps employed in both qualitative and quantitative research using the omics technologies that are pertinent to fungi characterisation. This stems from the understanding that data provided from the functional characterisation of fungi and their metabolites is important towards the techno-economic feasibility of large-scale production of biological products. The review further describes how the functional gaps left by genomics, internal transcribe spacer (ITS) regions are addressed by transcriptomics and the various techniques and platforms utilised, including quantitive reverse transcription polymerase chain reaction (RT-qPCR), hybridisation techniques, and RNA-seq, and the insights such data provide on the effect of environmental changes on fungal enzyme production from an expressional standpoint. The review also offers information on the many available bioinformatics tools of analysis necessary for the analysis of the overwhelming data synonymous with the omics approach to fungal characterisation.

Local Geomorphological Gradients and Land Use Patterns Play Key Role on the Soil Bacterial Community Diversity and Dynamics in the Highly Endemic Indigenous Afrotemperate Coastal Scarp Forest Biome.

Southern Afrotemperate forests are small multi-layered and highly fragmented biodiversity rich biomes that support unique flora and fauna endemism. However, little is known about the microbial community and their contribution to these ecosystems. In this study, high throughput sequencing analysis was used to investigate the soil bacterial community structure and function, and understand the effect of local topography/geomorphological formations and land use patterns on a coastal scarp forest. Soil samples were collected from three forest topography sites: upper (steeper gradients, 30-55°; open canopy cover, <30%), mid (less steep, 15-30°; continuous forest canopy, >80%), and lower (flatter gradient, <15°; open canopy cover, 20-65%), and from the adjacent sugarcane farms. Results indicated that forest soils were dominated by members of phyla Proteobacteria (mainly members of α-proteobacteria), Actinobacteria, Acidobacteria, Firmicutes, and Planctomycetes, while Actinobacteria and to a lesser extent ß-proteobacteria and γ-proteobacteria dominated SC soils. The core bacterial community clustered by habitat (forest vs. sugarcane farm) and differed significantly between the forest topography sites. The Rhizobiales (genera Variibacter, Bradyrhizobium, and unclassified Rhizobiales) and Rhodospirallales (unclassified Rhodospirillum DA111) were more abundant in forest mid and lower topographies. Steeper forest topography (forest_upper) characterized by the highly leached sandy/stony acidic soils, low in organic nutrients (C and N) and plant densities correlated to significant reduction of bacterial diversity and richness, associating significantly with members of order Burkholderiales (Burkholderia-Paraburkholderia, Delftia, and Massilia) as the key indicator taxa. In contrast, changes in the total nitrogen (TN), soil organic matter (SOM), and high acidity (low pH) significantly influenced bacterial community structure in sugarcane farm soils, with genus Acidothermus (Frankiales) and uncultured Solirubrobacterales YNFP111 were the most abundant indicator taxa. Availability of soil nutrients (TN and SOM) was the strongest driver of metabolic functions related to C fixation and metabolism, N and S cycling; these processes being significantly abundant in forest than sugarcane farm soils. Overall, these results revealed that the local topographical/geomorphological gradients and sugarcane farming affect both soil characteristics and forest vegetation (canopy coverage), that indirectly drives the structure and composition of bacterial communities in scarp forest soils.

Influences of geochemical factors and substrate availability on Gram-positive and Gram-negative bacterial distribution and bio-processes in ageing municipal landfills.

Bacteria are primary agents of organic substrate metabolisation and elemental cycling in landfills. Two major bacterial groups, namely, Gram-positive (GP) and Gram-negative (GN), drive independent metabolic functions that contribute to waste stabilisation. There is a lack of explicit exploration of how these different bacterial guilds respond to changing carbon (C) availability and substrate depletion as landfills age and how landfill geochemistry regulates their distribution. This study investigated and compared the abundance and vertical distribution of GP and GN bacteria in 14- and 36-year-old municipal landfills and explored linkages among bacterial groups, nutrient elements, heavy metals and soil texture. We found higher GP bacteria in the 14-year-old landfill, while GN bacteria dominated the 36-year-old landfill. The non-metric multidimensional scaling (nMDS) analysis showed that dissimilarities in the relative abundance of the GP and GN bacteria were linked distinctly to landfill age, and not depth. In support of this inference, we further found that GP and GN bacteria were negatively correlated with heavy metals and essential nutrients in the 14- and 36-year-old landfills, respectively. Notably, the GP/GN ratio, an indicator of relative C available for bacterial mineralisation, was greater in the14-year-old landfill, suggesting greater C availability. Conversely, the C to N ratio was higher in the 36-year-old landfill, indicating lower N mineralisation. Collectively, the results of the study reveal key insights into how landfill ageing and stabilisation influence distinct functional shifts in the abundance of GP and GN bacteria, and these are mainly driven by changes in C and N bioavailability.

Fungal and metabolome diversity of the rhizosphere and endosphere of Phragmites australis in an AMD-polluted environment.

Symbiotic associations with rhizospheric microbial communities coupled with the production of metabolites are key adaptive mechanisms by metallophytes to overcome metal stress. However, little is known about pseudometallophyte Phragmites australis interactions with fungal community despite commonly being applied in wetland phytoremediation of acid mine drainage (AMD). In this study, fungal community diversity and metabolomes production by rhizosphere and root endosphere of P. australis growing under three different AMD pollution gradient were analyzed. Our results highlight the following: 1) Ascomycota and Basidiomycota were dominant phyla, but the diversity and richness of taxa were lower within AMD sites with Penicillium, Candida, Saccharomycetales, Vishniacozyma, Trichoderma, Didymellaceae, and Cladosporium being enriched in the root endosphere and rhizosphere in AMD sites than non-AMD site; 2) non-metric multidimensional scaling (NMDS) of 73 metabolomes revealed spatially defined metabolite exudation by distinct root parts (rhizosphere vs endosphere) rather than AMD sites, with significant variability occurring within the rhizosphere correlating to pH, TDS, Fe, Cr, Cu and Zn content changes; 3) canonical correspondence analysis (CCA) confirmed specific rhizospheric fungal taxonomic changes are driven by pH, TDS, heavy metals, and stress-related metabolomes produced. This is the first report that gives a snapshot on the complex endophytic and rhizospheric fungal community structure and metabolites perturbations that may be key in the adaptability and metal phytoremediation by P. australis under AMD environment.

Shifts in Bacterial Diversity During the Spontaneous Fermentation of Maize Meal as Revealed by Targeted Amplicon Sequencing.

Maize meal was allowed to undergo uncontrolled fermentation in the laboratory, in simulation of the traditional method of fermentation as practised in most African households. During the fermentation process, samples were collected daily for 11 days. Physico-chemical analysis of the fermenting slurry and metagenomics analysis of the microbial community using 16S rRNA demonstrated an interrelationship between the changes in the properties of the fermentation environment and the successional interplay of the microbial community. The first 24 h of fermentation at pH of 6.5 was characterised by the proliferation of probiotic Lactobacillus and Bifidobacterium, with their relative abundance being 40.7% and 29.9%, respectively. However, prolonged fermentation and a drop in pH from 5.3 to 3.7 caused a decline and finally an absence of these probiotic bacteria which were replaced by Clostridium spp. with a relative abundance of between 97% and 99% from day 5 to day 11. This study demonstrated that prolonged fermentation of maize meal is not ideally suited for the proliferation of probiotic nutritionally beneficial bacteria.

Distribution and comparison of bacterial communities in HVAC systems of two university buildings: Implications for indoor air quality and public health.

The installation of HVAC systems in building is meant to enhance indoor air quality as well as increase comfort to occupants. However, HVAC systems have also become a vehicle of contamination of indoor air with potentially pathogenic microorganisms. DNA was extracted from ten HVAC filter dust samples collected from two buildings and subjected to high throughput sequencing analysis to determine the bacterial community structure. Further, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) software was used to predict the potential functional capabilities of the bacterial communities. Sequencing analysis led to the identification of five major bacterial phyla, including Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes and Bacteroidetes. At genus level, Mycobacterium, Bacillus, Cupriavidus, Hyphomicrobium and Mesorhizobium were the most dominant. With the exception of the later two bacterial genera, the first three are potential pathogens whose presence in HVAC systems poses a significant public health risk, especially among immunocompromised individuals. Nine pathways associated with antibiotics resistance and bacterial pathogenicity were identified, including polymyxin resistance and peptidoglycan biosynthesis pathways. Further, investigation of the relationship between the detected bacterial meta-communities and predicted potential virulence factors (antibiotic resistance and pathogenic genes) led to the detection of 350 positive associations among 43 core bacteria, 2 pathogenic genes (sitA and uidA) and 14 resistance genes. Overall, the heterogeneous nature of microorganisms found in HVAC systems observed in this study shows that HVAC systems are the origin of airborne infections in indoor environments, and must be periodically cleaned and disinfected to avoid the build-up of pathogens, and the subsequent exposure of human occupants of these pathogens.

Community diversity metrics, interactions, and metabolic functions of bacteria associated with municipal solid waste landfills at different maturation stages.

Municipal landfills are hot spots of dynamic bioprocesses facilitated by complex interactions of a multifaceted microbiome, whose functioning in municipal landfills at different maturing stages is poorly understood. This study determined bacterial community composition, interaction conetworks, metabolic functions, and controlling physicochemical properties in two landfills aged 14 and 36 years. High throughput sequencing revealed a similar distribution of bacterial diversity, evenness, and richness in the 14- and 36-year-old landfills in the 0-90 cm depth. At deeper layers (120-150 cm), the 14-year-old landfill had significantly greater bacterial diversity and richness indicating that it is a more active microcosm than the 36-year-old landfill, where phylum Epsilonbacteraeota was overwhelmingly dominant. The taxonomic and functional diversity in the 14-year-old landfill was further reflected by the abundant presence of indicator genera Pseudomonas,Lutispora,Hydrogenspora, and Sulfurimonas coupled with the presence of biomarker enzymes associated with carbon (C), nitrogen (N), and sulfur (S) metabolism. Furthermore, canonical correspondence analysis revealed that bacteria in the 14-year-old landfill were positively correlated with high C, N, S, and phosphorus resulting in positive cooccurrence interactions. In the 36-year-old landfill, negative coexclusion interactions populated by members of N fixing Rhizobiales were dominant, with metabolic functions and biomarker enzymes predicting significant N fixation that, as indicated by interaction network, potentially inhibited ammonia-intolerant bacteria. Overall, our findings show that diverse bacterial community in the 14-year-old landfill was dominated by copiotrophs associated with positive conetworks, whereas the 36-year-old landfill was dominated by lithotrophs linked to coexclusion interactions that greatly reduced bacterial diversity and richness.