Diversity of bacteria and archaea from a landfill in Chandigarh, India as revealed by culture-dependent and culture-independent molecular approaches

Microbial diversity and potential health risks of household municipal solid waste in China: A case study in winter during outbreak of COVID-19

Microbial (bacteria and fungi) community structures and their distributions in urban household municipal solid waste (HMSW) were characterized in a sampling campaign in 38 cities of China covering 5 climatic zones. All samples were collected from garbage containers in residential communities during the Winter of 2022, from January 11 to 26. A total of 247 bacterial genera belonging to 22 phyla were identified among the samples. Firmicutes (44.3 %), Bacteroidetes (33.77 %) and Proteobacteria (21.54 %) were the top 3 dominant phyla, and Arcicella (33.11 %) and Leuconostoc (21.87 %) were the dominant genera. Meanwhile, 124 fungal genera from 7 fungal phyla were detected. Ascomycota was the most dominant phylum, with an average relative abundance of 77.31 %. Hanseniaspora (24.03 %), Debaryomyces (13.47 %), Candida (12.18) were the top 3 dominant fungal genera. Alpha-diversity analysis showed that the species richness and diversity of bacterial and fungal communities of HMSW samples belonging to different climatic zones did not differ significantly. Nonmetric multidimensional scaling (NMDS) analysis confirmed that climatic had an effect on microbial communities but did not show a significant correlation. In addition, the distribution of microbial community in different samples from the same climate zone varied considerably, suggesting the HMSW source play important role in shaping microbial community composition. Considering that residential HMSW is relatively fresh, we speculates that the original microorganisms residing in different components of HMSW are key influencing factor for the community, while the reshaping force driven by environmental conditions are relatively weak. In addition, the study identified 13 bacterial and 16 fungal pathogens with Pseudomonas putida (0.25 %) and Sclerotinia sclerotiorum (2.12 %) as the most abundant potential pathogenic bacteria and fungi, respectively. These findings provide valuable information for characterizing microbial features and potential risks of HMSW in its management system.

The exposure risks associated with pathogens and antibiotic resistance genes in bioaerosol from municipal landfill and surrounding area

Pathogenic microbes with antibiotic resistance can thrive on municipal solid waste as nutrients and be aerosolized and transported to vicinities during waste disposal processes. However, the characterization of pathogenic bioaerosols and assessment of their exposure risks are lacking. Herein, particle size, concentration, activity, antibiotic resistance, and pathogenicity of airborne microorganisms were assessed in different sectors of a typical landfill. Results showed that active sector in downwind direction has the highest bioaerosol level (1234 CFU/m³), while residential area has the highest activity (14.82 mg/L). Botanical deodorizer from mist cannon can effectively remove bioaerosol. Most bioaerosols can be inhaled into respiratory system till bronchi with sizes ranging from 2.1-3.3 and 3.3-4.7 µm. Pathogenic bacteria (Bacilli, Bacillus, and Burkholderia-Paraburkholderia) and allergenic fungi (Aspergillus, Cladosporium, and Curvularia) prevailed in landfill. Although high abundance of microbial volatile organic compounds (mVOCs) producing bioaerosols were detected, these mVOCs contributed little to odor issues in landfill. Notably, surrounding areas have higher levels of antibiotic-resistance genes (ARGs) than inner landfill with tetC, acrB, acrF, mdtF, and bacA as dominant ones. Most ARGs were significantly correlated with bacterial community, while environmental parameters mainly influenced fungal prevalence. These findings can assist in reducing and preventing respiratory allergy or infection risks in occupational environments relating to waste management.

A case study of environmental pollution by pathogenic bacteria and metal(oid)s at Soran Landfill Site, Erbil, Iraqi Kurdistan Region

Environmental pollution is a serious issue all around the world, especially when it is caused by metal(oid)s and pathogenic microorganisms. This study reports here for the first time on the contamination of soil and water with metal(oid)s and pathogenic bacteria directly resulting from the Soran Landfill Site. Soran landfill is a level 2 solid waste disposal site that lacks leachate collection infrastructure. The site is potentially an environmental and public hazard caused by metal(oid)s content and significantly dangerous pathogenic microorganisms through leachate release into the soil and nearby river. This study reports on the levels of the metal(oid)s content of As, Cd, Co, Cr, Cu, Mn, Mo, Pb, Zn, and Ni obtained by inductively coupled plasma mass spectrometer in soil, leachate stream mud, and leachate samples. Five pollution indices are used to assess potential environmental risks. According to the indices, Cd and Pb contamination is significant, whereas As, Cu, Mn, Mo, and Zn pollution is moderate. A total of 32 isolates of bacteria were defined from soil, leachate stream mud, and liquid leachate samples: 18, 9, and 5, respectively. Moreover, 16 s rRNA analysis suggested that the isolates belong to three enteric bacterial phyla of Proteobacteria, Actinobacteria, and Firmicutes. The closest GenBank matches of 16S rDNA sequences indicated the presence of the genera: Pseudomonas, Bacillus, Lysinibacillus, Exiguobacterium, Trichococcus, Providencia, Enterococcus, Macrococcus, Serratia, Salinicoccus, Proteus, Rhodococcus, Brevibacterium, Shigella, Micrococcus, Morganella, Corynebacterium, Escherichia, and Acinetobacter. The identity percentage was mostly between 95%-100%. The results of this study show the levels of microbiological and geochemical contamination of soils, surface and potentially ground water with harmful microorganisms and toxic metal(oid)s originating specifically from Soran landfill leachate which subsequently incorporated into the surrounding environment, creating thus a considerable health and environmental risk.

Landfill: An eclectic review on structure, reactions and remediation approach

Since the enactment of the Clean Water Act (1972), which was supplemented by increased accountability under Resource Conservation and Recovery Act (RCRA) Subtitle D (1991) and the Clean Air Act Amendments (1996), landfills have indeed been widely used all around the world for treating various wastes. The landfill's biological and biogeochemical processes are believed to be originated about 2 to 4 decades ago. Scopus and web of Science based bibliometric study reveals that there are few papers available in scientific domain. Further, till today not a single paper demonstrated the detailed landfills heterogenicity, chemistry and microbiological processes and their associated dynamics in a combined approach. Accordingly, the paper addresses the recent applications of cutting-edge biogeochemical and biological methods adopted by different countries to sketch an emerging perspective of landfill biological and biogeochemical reactions and dynamics. Additionally, the significance of several regulatory factors controlling the landfill's biogeochemical and biological processes is highlighted. Finally, this article emphasizes the future opportunities for integrating advanced techniques to explain landfill chemistry explicitly. In conclusion, this paper will provide a comprehensive vision of the diverse dimensions of landfill biological and biogeochemical reactions and dynamics to the scientific world and policymakers.

Environmental impacts of an unlined municipal solid waste landfill on groundwater and surface water quality in Ibadan, Nigeria

Environmental and public health concerns grow on the interaction of municipal solid waste (MSW) leachates from unlined waste disposal sites with aquifers in many developing countries. This study investigated the environmental pollution impacts of an unlined MSW landfill at Ajakanga area, Ibadan, southwest Nigeria. Analytical studies indicated that the concentrations of NO₃^-, SO₄^2-, PO₄^3-, NH₄^-, Cl^-, Na, Fe, Mn, Cr, and Mo in the leachate samples exceeded the WHO wastewater discharge limits. Hydrochemical parameters of the groundwater and surface water were within WHO allowable thresholds, except for EC, TDS, Fe, Mn, and Pb in the groundwater and Pb, Cd, and Cu in the surface water, indicating major geogenic and minor MSW leachate impacts on the groundwater and surface water chemistry. Bacteria found in the leachate include Enterobacter cloacae (16.67%), Pseudomonas spp. (14.28%) and Bacillus spp. (9.52%). The geoelectrical imaging data indicated substratum leachate infiltration greater than 10 m deep, which is consistent with the low resistivity values of the topsoil-weathered basement layers. The health risk assessment showed high hazardous index values, indicating health risks of Mn, Cd and Pb in the surface water for the residents around Ajakanga landfill. Hydrochemical data indicated greater impact of the MSW leachates on the surface water than the groundwater, while geophysical data showed greater propensity of the surrounding aquifer to leachate interaction through fractured basement zone with increasing abstraction. Waste site closure and hydrochemical monitoring are suggested measures to mitigate environmental pollution in the study area.

A culture-based and culture-independent approach to the study of landfill leachate bacterial and archaeal communities

The landfill is a convenient and affordable method of municipal solid waste (MSW) management. Landfill leachate contains a heavy load of pollutants and pathogens. Discharge of untreated leachate is the leading cause of surface and groundwater contamination and a threat to public and environmental health. To develop an efficient leachate treatment technology, an in-depth understanding of landfill chemistry and microbiology is essential. In the present manuscript, we conducted a comparative study of three different landfill leachate samples using cultivation-based and culture-independent molecular studies. We cultivated 85 species of aerobic, anaerobic bacteria and archaea from leachate represented by a total of 200 strains using extensive culturomics approaches. Twelve out of 200 cultivated strains of bacteria showed very low 16S rRNA gene sequence similarity (84-98.6%) with their closest relatives and could be the potential novel taxa, the first time cultivated from leachate. Members of the six genera only have 2-5 representatives from past studies from other habitats but first time cultivated from leachate. In addition to bacteria, we also cultivated and characterized different groups of methanogenic archaea. Our chemistry data indicate that leachate is a highly stressed ecosystem with an assemblage of many toxic wastes like sulfur, zinc, mercury, chromium, etc. 16S rRNA gene-based amplicon analysis showed the dominance of (30-55%) methanogens and haloarachaea. Our data suggest that archaea are the significant regulators of leachate ecology, and more in-depth studies with multiple leachate samples are required to understand their role in leachate nutrient cycling and the development of effective leachate treatment technology.

Microbial Treatment of Raw and Primary Treated Sanitary Landfill Leachate by Indigenous Strain Brevibacillus agri

Landfill leachate is a potential environmental threat. Sanitary landfills are model sites which contains a leachate collection pool and a processing facility to treat it up to environmental standards before discharge. The present study is the very first endeavor to establish leachate treatment efficiency of indigenous microbial strain Brevibacillus agri. Leachate samples were inoculated with isolated strain and incubated for 41 days in an orbital shaker. Percent reduction in major water quality parameters was assessed after 0, 7, 21, and 41 days of incubation, for understanding the degradation kinetics. Results of the study demonstrate that Brevibacillus agri was effective in improving the wastewater quality of both raw and primary treated leachate. Overall reduction for different water quality parameters was found to be 50% higher for primary treated leachate than that for raw leachate within 21 days of incubation. Microbial degradation followed first-order kinetics with rate constants in the range of 0.0047-0.03 and 0.0061-0.074 day^-1 for raw and primary treated leachate respectively. Calculated half-life of each pollutant parameter was significantly higher in the raw sample (23-147 days) as compared to the primary treated one (27-112 days). The leachate pollution index (LPI) value of the raw leachate was also found to be > 25% higher than primary treated leachate sample after microbial treatment. Hence, it can be concluded that on site application of primary treatment technology followed by secondary microbial degradation by indigenous microflora, viz., Brevibacillus sp., may prove effective to achieve desirable water quality for safe environmental discharge.

Biogeochemical profiling and taxonomic characterization of municipal landfill site by metagenomic sequencing

Most of the discarded waste material paves their way to the utmost common dumping grounds, Landfills. Despite their widespread use, the landfill microbiomes are still not well characterized. Metagenomics approach provides insight into the identification of operational parameters influencing the microbiome composition and their biodegradation competencies. The metagenomic DNA was prepared to explore taxonomical community structure, phylogenetic relationships, and functional profile at the same time. A total of 100,021,052 high-quality filtered reads were acquired with a GC abundance of 62.59%. Taxonomical abundance revealed the dominance of phylum Proteobacteria and genes involved in biomolecules metabolism, aromatic compound degradation, stress tolerance, xenobiotic biodegradation etc. were revealed functionally. The intricate heterogeneous environment of landfill revealed well flourished biogeochemical metabolic profiles including nitrogen metabolism. This is the first study for the generated metagenome of Ghazipur landfill and the obtained results propose that microbial communities in landfill settings are far more intricate than expected. It remain mostly unexplored which demands the usage of multiple platforms for a better understanding.

Assessment of Physicochemical, Microbiological and Toxicological Hazards at an Illegal Landfill in Central Poland

This study aimed to assess the physicochemical, microbiological and toxicological hazards at an illegal landfill in central Poland. The research included the analysis of airborne dust (laser photometer), the number of microorganisms in the air, soil and leachate (culture method) and the microbial diversity in the landfill environment (high-throughput sequencing on the Illumina Miseq); the cytotoxicity (PrestoBlue) and genotoxicity (alkaline comet assay) of soil and leachate were tested. Moreover, an analysis of UHPLC-Q-ToF-UHRMS (ultra-high-performance liquid chromatography-quadrupole-time-of-flight ultrahigh-resolution mass spectrometry) was performed to determine the toxic compounds and microbial metabolites. The PM₁ dust fraction constituted 99.89% and 99.99% of total dust and exceeded the threshold of 0.025 mg m⁻³ at the tested locations. In the air, the total number of bacteria was 9.33 × 10¹–1.11 × 10³ CFU m⁻³, while fungi ranged from 1.17 × 10² to 4.73 × 10² CFU m⁻³. Psychrophilic bacteria were detected in the largest number in leachates (3.3 × 10⁴ to 2.69 × 10⁶ CFU mL⁻¹) and in soil samples (8.53 × 10⁵ to 1.28 × 10⁶ CFU g⁻¹). Bacteria belonging to Proteobacteria (42–64.7%), Bacteroidetes (4.2–23.7%), Actinobacteria (3.4–19.8%) and Firmicutes (0.7–6.3%) dominated. In the case of fungi, Basidiomycota (23.3–27.7%), Ascomycota (5.6–46.3%) and Mortierellomycota (3.1%) have the highest abundance. Bacteria (Bacillus, Clostridium, Cellulosimicrobium, Escherichia, Pseudomonas) and fungi (Microascus, Chrysosporium, Candida, Malassezia, Aspergillus, Alternaria, Fusarium, Stachybotrys, Cladosporium, Didymella) that are potentially hazardous to human health were detected in samples collected from the landfill. Tested leachates and soils were characterised by varied cyto/genotoxins. Common pesticides (carbamazepine, prometryn, terbutryn, permethrin, carbanilide, pyrethrin, carbaryl and prallethrin), quaternary ammonium compounds (benzalkonium chlorides), chemicals and/or polymer degradation products (melamine, triphenylphosphate, diphenylphtalate, insect repellent diethyltoluamide, and drugs (ketoprofen)) were found in soil and leachate samples. It has been proven that the tested landfill is the source of the emission of particulate matter; microorganisms (including potential pathogens) and cyto/genotoxic compounds.

Destruction of the soil microbial ecological environment caused by the over-utilization of the rice-crayfish co-cropping pattern

The rice-crayfish co-cropping pattern is a traditional method for the intensive utilization of rice fields. In recent years, this pattern has been over-developed in many countries and regions, especially in China, because of its simple agronomic technology and high economic benefits. However, little is known about the potential ecological problems regarding soil microorganisms caused by the over-utilization of this pattern. The results show that rice-crayfish co-cropping, when over-utilized for a long time, reduced soil microbial richness and diversity compared with rice monocropping. A decrease in bacterial abundance in the nitrogen cycle and an increase in bacterial abundance in the carbon cycle led to a decrease in the nitrogen cycle function and an increase in the carbon cycle function. In an analysis of bacteria that are sensitive to cropping patterns, it was found that in the rice-crayfish co-cropping, the relative abundances of sensitive OTUs from Firmicutes (Bacillus and Clostridium) and Chloroflexi (Anaerolineaceae) were significantly higher during the entire growth period than those observed in the rice monocropping pattern, while the relative abundances of sensitive OTUs from Nitrospirae (Nitrospira), Gemmatimonadetes (Gemmatimonas), and Actinobacteria (Nocardioides) were significantly lower than those observed in the rice monocropping pattern. A network analysis shows that growth-period-sensitive OTUs drive the co-occurrence network modules, although the OTUs also have positive and negative correlations among modules but a positive synergistic effect on the regulation of soil nutrients. In addition, OTUs that were sensitive at the booting stage and filling stage were the key microbial groups in the rice-crayfish co-cropping and rice monocropping networks, respectively. Understanding the classifications and functions of sensitive microbes present during the rice growth period is the basis for formulating a microbial flora management strategy for the rice-crayfish co-cropping pattern, which is of great significance for adjusting agricultural management measures and controlling current soil microbial ecological problems.

Insights into the stabilization of landfill by assessing the diversity and dynamic succession of bacterial community and its associated bio-metabolic process

The distribution of bacterial community in an actual landfill was analyzed and the bioprocess involved in refuse degradation was clarified. The results showed that the degradation degree of refuse showed great differences with the landfill age, in which the contents of organic matter (OM) and total Kjeldahl nitrogen (TKN) in refuse as well as the chemical oxygen demand (COD) in leachate presented decreasing trends with increasing landfill age. The diversity of bacterial community increased first and then decreased with increasing landfill age. The main bacterial phyla involved in refuse degradation were Proteobacteria, Firmicutes and Bacteroidetes, among which, Proteobacteria had an absolute advantage with a relative abundance ranging of 66-78%. With increasing landfill age, the abundance of Firmicutes decreased gradually, while that of Bacteroidetes increased. Pseudomonas, Thiopseudomonas, Psychrobacter and Desemzia were the main genera. The distribution of bacterial community in samples with landfill ages of 0-1 and 1-3 years were greatly influenced by TKN and pH, respectively. Amino acid and carbohydrate metabolism were the main biological pathways according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the biodegradation of xenobiotics as well as terpenoids and polyketides also accounted relatively high frequencies in the landfill. These results provide a better understanding of landfill microbiology and bioprocesses for landfill stabilization.

Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology

The role of methane as a greenhouse gas in the concept of global climate changes is well known. Methanogens and methanotrophs are two microbial groups which contribute to the biogeochemical methane cycle in soil, so that the total emission of CH4 is the balance between its production and oxidation by microbial communities. Traditional identification techniques, such as selective enrichment and pure-culture isolation, have been used for a long time to study diversity of methanogens and methanotrophs. However, these techniques are characterized by significant limitations, since only a relatively small fraction of the microbial community could be cultured. Modern molecular methods for quantitative analysis of the microbial community such as real-time PCR (Polymerase chain reaction), DNA fingerprints and methods based on high-throughput sequencing together with different “omics” techniques overcome the limitations imposed by culture-dependent approaches and provide new insights into the diversity and ecology of microbial communities in the methane cycle. Here, we review available knowledge concerning the abundances, composition, and activity of methanogenic and methanotrophic communities in a wide range of natural and anthropogenic environments. We suggest that incorporation of microbial data could fill the existing microbiological gaps in methane flux modeling, and significantly increase the predictive power of models for different environments.

Bioaerosols in the landfill environment: an overview of microbial diversity and potential health hazards

Landfilling is one of the indispensable parts of solid waste management in various countries. Solid waste disposed of in landfill sites provides nutrients for the proliferation of pathogenic microbes which are aerosolized into the atmosphere due to the local meteorology and various waste disposal activities. Bioaerosols released from landfill sites can create health issues for employees and adjoining public. The present study offers an overview of the microbial diversity reported in the air samples collected from various landfill sites worldwide. This paper also discusses other aspects, including effect of meteorological conditions on the bioaerosol concentrations, sampling techniques, bioaerosol exposure and potential health impacts. Analysis of literature concluded that landfill air is dominated by microbial dust or various pathogenic microbes like Enterobacteriaceae, Staphylococcus aureus, Clostridium perfringens, Acinetobacter calcoaceticus and Aspergillus fumigatus. The bioaerosols present in the landfill environment are of respirable sizes and can penetrate deep into lower respiratory systems and trigger respiratory symptoms and chronic pulmonary diseases. Most studies reported higher bioaerosol concentrations in spring and summer as higher temperature and relative humidity provide a favourable environment for survival and multiplication of microbes. Landfill workers involved in solid waste disposal activities are at the highest risk of exposure to these bioaerosols due to their proximity to solid waste and as they practise minimum personal safety and hygiene measures during working hours. Workers are recommended to use personal protective equipment and practise hygiene to reduce the impact of occupational exposure to bioaerosols.

Microbial structure and diversity in non-sanitary landfills and association with physicochemical parameters

This study assessed the bacterial populations in a non-sanitary landfill around Guarani Aquifer recharge zone in Brazil. Samples from two different positions (sites 1 and 2) at three different depths were evaluated, totaling six solid waste samples; two samples from an impacted stream were also collected. 16S rRNA sequencing was performed using the Ion S5TM XL platform; 3113 operational taxonomic units (OTUs) and 52 phyla were identified. Proteobacteria (37%) and Firmicutes (28%) were the most abundant phyla in the landfill, whereas Proteobacteria (~ 50%) and Bacteroidetes (~ 10%) were more profuse in surface water samples. Canonical correlation analysis (CCA) enabled us to clearly separate the samples according to their spatial location (site 1 or 2) or environmental matrix (surface water or solid waste samples), showing that microbiological populations are strongly associated with site-specific conditions and the kind of environmental matrix they come from. Environmental factors that mostly influenced the microbial communities were organic matter, oxidation-reduction potential, moisture, alkalinity, nitrogen (TKN), sodium, potassium, and zinc. Exiguobacterium (phylum Firmicutes) was overwhelmingly dominant at site 1 and was associated with higher concentrations of organic matter and potassium. Differently, site 2 did not present such dominant genera and was more diverse having lower concentrations of organic matter and nutrients. Distinct environments co-exist inside the same waste deposit, including zones which are representative of active and closed landfills and the occurrence of considerable physicochemical and microbiological shifts within short distances. Those shifts indicate that microbial populations are well adapted to the heterogeneity typical of urban solid waste, which is possibly beneficial to contaminant degradation. Graphical abstract.

A Review of Landfill Microbiology and Ecology: A Call for Modernization With 'Next Generation' Technology

Engineered and monitored sanitary landfills have been widespread in the United States since the passage of the Clean Water Act (1972) with additional controls under RCRA Subtitle D (1991) and the Clean Air Act Amendments (1996). Concurrently, many common perceptions regarding landfill biogeochemical and microbiological processes and estimated rates of gas production also date from 2 to 4 decades ago. Herein, we summarize the recent application of modern microbiological tools as well as recent metadata analysis using California, USEPA and international data to outline an evolving view of landfill biogeochemical/microbiological processes and rates. We focus on United States landfills because these are uniformly subject to stringent national and state requirements for design, operations, monitoring, and reporting. From a microbiological perspective, because anoxic conditions and methanogenesis are rapidly established after daily burial of waste and application of cover soil, the >1000 United States landfills with thicknesses up to >100 m form a large ubiquitous group of dispersed 'dark' ecosystems dominated by anaerobic microbial decomposition pathways for food, garden waste, and paper substrates. We review past findings of landfill ecosystem processes, and reflect on the potential impact that application of modern sequencing technologies (e.g., high throughput platforms) could have on this area of research. Moreover, due to the ever evolving composition of landfilled waste reflecting transient societal practices, we also consider unusual microbial processes known or suspected to occur in landfill settings, and posit areas of research that will be needed in coming decades. With growing concerns about greenhouse gas emissions and controls, the increase of chemicals of emerging concern in the waste stream, and the potential resource that waste streams represent, application of modernized molecular and microbiological methods to landfill ecosystem research is of paramount importance.

NGS-based characterization of microbial diversity and functional profiling of solid tannery waste metagenomes

Tanneries pose a serious threat to the environment by generating large amount of solid tannery waste (STW). Two metagenomes representing tannery waste dumpsites Jajmau (JJK) and Unnao (UNK) were sequenced using Illumina HiSeq platform. Microbial diversity analysis revealed domination of Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Planctomycetes in both metagenomes. Presence of pollutant degrading microbes such as Bacillus, Clostridium, Halanaerobium and Pseudomonas strongly indicated their bioremediation ability. KEGG and SEED annotated main functional categories included carbohydrate metabolism, amino acids metabolism, and protein metabolism. KEGG displayed 5848 and 9633 proteases encoding ORFs compared to 5159 and 8044 ORFs displayed by SEED classification in JJK and UNK metagenomes, respectively. Abundantly present serine- and metallo-proteases belonging to Bacillaceae, Clostridiaceae, Xanthomonadaceae, Flavobacteriaceae and Chitinophagaceae families exhibited proteinaceous waste degrading ability of these metagenomes. Further structural and functional analysis of metagenome encoded enzymes may facilitate the discovery of novel proteases useful in bioremediation of STW.

Taxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade

Microbial taxonomy dealing with identification and characterization of prokaryotes like bacteria and archaea has always been a major area of research all over the world. Exploring diversity of microbes and description of novel species with different genes and secondary compounds is of utmost importance for better future and sustenance of life. India having an enormous range of ecosystems and diverse species inhabiting these niches is considered to be one of the richest biodiversity regions of the world. During the last decade, with newer methodologies and better technology, the prokaryotic taxonomy from India has extended our inventory of microbial communities in specific niches. However, there still exist some limitations in classifying the microbes from India as compared to that is done world-over. This review enlists the taxonomic description of novel taxa of prokaryotes from India in the past decade. A total of 378 new bacterial species have been classified from different habitats in India in the last ten years and no descriptions of archaeal species is documented till date.

Assessment of groundwater pollution near Aba-Eku municipal solid waste dumpsite

Municipal solid waste (MSW) dumpsite constitutes a major anthropogenic point source of leachate contamination to the ambient groundwater and poses a significant threat to the geo-ecosystem. This study investigated the pollution of groundwater by leachate emanating from Aba-Eku MSW dumpsite in Ibadan, Nigeria, using bacteriological, hydrochemical, and geophysical techniques. There is a diversity of bacteria in the leachate and the dominant phyla being proteobacteria (83%) and firmicutes (17%). The mean concentrations (mg/L) of Mn, Fe, Al, Cu, Mo, and Cr in the leachate samples were above the World Health Organization wastewater discharge limits. The hydrochemical parameters of the groundwater samples around the dumpsite were generally within the permissible limits, except for K and Cl^-; which invariably indicate major inputs from water-rock interaction and minor contributions from the dumpsite. Three geoelectrical layers were indicated from the vertical electrical sounding data, which are the topsoil, the lateritic clay layer, and the weathered basement. Low resistivity values of 5-33 Ωm and 3-24 Ωm were obtained within 2 m and 5.5 m depths for the topsoil and the lateritic layer, respectively; while the 2-D subsurface model reveals leachate plume beyond 5 m. Although the MSW leachate is heterogeneous, the hydrochemical data show that the aquifer around the dumpsite has not been seriously polluted with the leachate, but there is a continuous percolation of leachate into the soil subsurface, based on the geophysical findings. Discontinuing waste dumping and groundwater extraction, which would over time reduce the leachate plume, are measures to enhance the groundwater quality in the area.

Microbiology of municipal solid waste landfills: a review of microbial dynamics and ecological influences in waste bioprocessing

Municipal solid waste landfills are widely used as a waste management tool and landfill microbiology is at the core of waste degradation in these ecosystems. This review investigates the microbiology of municipal solid waste landfills, focusing on the current state of knowledge pertaining to microbial diversity and functions facilitating in situ waste bioprocessing, as well as ecological factors influencing microbial dynamics in landfills. Bioprocessing of waste in municipal landfills emanates from substrate metabolism and co-metabolism by several syntrophic microorganisms, resulting in partial transformation of complex substrates into simpler polymeric compounds and complete mineralisation into inorganic salts, water and gases including the biofuel gas methane. The substrate decomposition is characterised by evolution and interactions of different bacterial, archaeal and fungal groups due to prevailing biotic and abiotic conditions in the landfills, allowing for hydrolytic, fermentative, acetogenic and methanogenic processes to occur. Application of metagenomics studies based on high throughput Next Generation Sequencing technique has advanced research on profiling of the microbial communities in municipal solid waste landfills. However, functional diversity and bioprocess dynamics, as well as key factors influencing the in situ bioprocesses involved in landfill waste degradation; the very elements that are key in determining the efficiency of municipal landfills as tools of waste management, remain ambiguous. Such gaps also hinder progressive understanding of fundamentals that underlie technology development based on waste biodegradation, and exploration of municipal waste as a bioresource.

Succession and diversity of microbial communities in landfills with depths and ages and its association with dissolved organic matter and heavy metals

Landfill is an important method for the treatment of municipal solid wastes. Microbes play a central role in the biodegradation and stabilization of organic matter during landfill; however, the succession of microbial communities in landfills and their association with organic matter still remain unclear. This study investigated the succession and diversity of microorganisms in landfill depending on different depths and ages as well as its association with dissolved organic matter (DOM) and heavy metals. The results showed that the actinobacterial diversity and richness were high compared to bacteria in young landfill cells. The diversity and richness of bacteria and actinobacterial were the highest in the middle layer in the intermediate and old landfill cells. Firmicutes, Proteobacteria, and Actinobacteria were the most dominant phyla. Firmicutes were mainly affected by the humification degree, and the aromatic and protein-like substance content of the landfill-derived DOM. The phylum Proteobacteria was greatly affected by the lipid and humic-like substances content of the landfill-derived DOM, while the distribution of Actinobacteria was regulated by both aromatic and humic-like substances. The effect of dissolved heavy metals on the microbial distribution in landfill differed for the metals Cr, Ni, Pb, Mn, Cu, Zn, and Cd. Siderophile elements (Cr, Ni, and Pb) were necessary trace elements for Proteobacteria and Actinobacteria, and promoted their growth. Oxyphilic element (Mn) was an important factor promoting the growth of Actinobacteria. However, no apparent relationship was found between sulfurophile elements (Cu, Zn, and Cd) and microorganisms.

Examination into the taxonomic position of Bacillus thermotolerans Yang et al., 2013, proposal for its reclassification into a new genus and species Quasibacillus thermotolerans gen. nov., comb. nov. and reclassification of B. encimensis Dastager et al., 2015 as a later heterotypic synonym of B. badius

Two novel Gram-staining positive, rod-shaped, moderately halotolerant, endospore forming bacterial strains 5.5LF 38TD and 5.5LF 48TD were isolated and taxonomically characterized from a landfill in Chandigarh, India. The analysis of 16S rRNA gene sequences of the strains confirmed their closest identity to Bacillus thermotolerans SgZ-8T with 99.9% sequence similarity. A comparative phylogenetic analysis of strains 5.5LF 38TD, 5.5LF 48TD and B. thermotolerans SgZ-8^T confirmed their separation into a novel genus with B. badius and genus Domibacillus as the closest phylogenetic relatives. The major fatty acids of the strains are iso-C_15:0 and iso-C_16:0 and MK-7 is the only quinone. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The digital DNA-DNA hybridization (DDH) and ortho average nucleotide identity (ANI) values calculated through whole genome sequences indicated that the three strains showed low relatedness with their phylogenetic neighbours. Based on evidences from phylogenomic analyses and polyphasic taxonomic characterization we propose reclassification of the species B. thermotolerans into a novel genus named Quasibacillus thermotolerans gen. nov., comb. nov with the type strain SgZ-8^T (=CCTCC AB2012108^T=KACC 16706^T). Further our analyses also revealed that B. encimensis SGD-V-25^T is a later heterotypic synonym of Bacillus badius DSM 23^T.

Microbial community structure and diversity in a municipal solid waste landfill

Municipal solid waste (MSW) landfills are the most prevalent waste disposal method and constitute one of the largest sources of anthropogenic methane emissions in the world. Microbial activities in disposed waste play a crucial role in greenhouse gas emissions; however, only a few studies have examined metagenomic microbial profiles in landfills. Here, the MiSeq high-throughput sequencing method was applied for the first time to examine microbial diversity of the cover soil and stored waste located at different depths (0-150cm) in a typical MSW landfill in Yangzhou City, East China. The abundance of microorganisms in the cover soil (0-30cm) was the lowest among all samples, whereas that in stored waste decreased from the top to the middle layer (30-90cm) and then increased from the middle to the bottom layer (90-150cm). In total, 14 phyla and 18 genera were found in the landfill. A microbial diversity analysis showed that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla, whereas Halanaerobium, Methylohalobius, Syntrophomonas, Fastidiosipila, and Spirochaeta were the dominant genera. Methylohalobius (methanotrophs) was more abundant in the cover layers of soil than in stored waste, whereas Syntrophomonas and Fastidiosipila, which affect methane production, were more abundant in the middle to bottom layers (90-150cm) in stored waste. A canonical correlation analysis showed that microbial diversity in the landfill was most strongly correlated with the conductivity, organic matter, and moisture content of the stored waste.

Composition of bacterial and archaeal communities during landfill refuse decomposition processes

Little is known about the archaeal and the bacterial diversities in a landfill during different phases of decomposition. In this study, the archaeal and the bacterial diversities of Laogang landfill (Shanghai, China) at two different decomposition phases (i.e., initial methanogenic phase (IMP) and stable methanogenic phase (SMP)), were culture-independently examined using PCR-based 454 pyrosequencing. A total of 47,753 sequences of 16S rRNA genes were retrieved from 69,954 reads and analyzed to evaluate the diversities of the archaeal and bacterial communities. The most predominant types of archaea were hydrogenotrophic Methanomicrobiales, and of bacteria were Proteobacteria, Firmicutes, and Bacteroidetes. As might be expected, their abundances varied at decomposition phases. Archaea Methanomicrobiales accounts for 97.6% of total archaeal population abundance in IMP and about 57.6% in SMP. The abundance of archaeal genus Halobacteriale was 0.1% in IMP and was 20.3% in the SMP. The abundance of Firmicutes was 21.3% in IMP and was 4.3% in SMP. The abundance of Bacteroidetes represented 11.5% of total bacterial in IMP and was dominant (49.4%) in SMP. Both the IMP and SMP had unique cellulolytic bacteria compositions. IMP consisted of members of Bacillus, Fibrobacter, and Eubacterium, while SMP harbored groups of Microbacterium. Both phases had Clostridium with different abundance, 4-5 folds higher in SMP.

Wastewater irrigation increases the abundance of potentially harmful gammaproteobacteria in soils in Mezquital Valley, Mexico

Wastewater contains large amounts of pharmaceuticals, pathogens, and antimicrobial resistance determinants. Only a little is known about the dissemination of resistance determinants and changes in soil microbial communities affected by wastewater irrigation. Community DNAs from Mezquital Valley soils under irrigation with untreated wastewater for 0 to 100 years were analyzed by quantitative real-time PCR for the presence of sul genes, encoding resistance to sulfonamides. Amplicon sequencing of bacterial 16S rRNA genes from community DNAs from soils irrigated for 0, 8, 10, 85, and 100 years was performed and revealed a 14% increase of the relative abundance of Proteobacteria in rainy season soils and a 26.7% increase in dry season soils for soils irrigated for 100 years with wastewater. In particular, Gammaproteobacteria, including potential pathogens, such as Pseudomonas, Stenotrophomonas, and Acinetobacter spp., were found in wastewater-irrigated fields. 16S rRNA gene sequencing of 96 isolates from soils irrigated with wastewater for 100 years (48 from dry and 48 from rainy season soils) revealed that 46% were affiliated with the Gammaproteobacteria (mainly potentially pathogenic Stenotrophomonas strains) and 50% with the Bacilli, whereas all 96 isolates from rain-fed soils (48 from dry and 48 from rainy season soils) were affiliated with the Bacilli. Up to six types of antibiotic resistance were found in isolates from wastewater-irrigated soils; sulfamethoxazole resistance was the most abundant (33.3% of the isolates), followed by oxacillin resistance (21.9% of the isolates). In summary, we detected an increase of potentially harmful bacteria and a larger incidence of resistance determinants in wastewater-irrigated soils, which might result in health risks for farm workers and consumers of wastewater-irrigated crops.