Thermophilic bacterial communities inhabiting the microbial mats of "indifferent" and chalybeate (iron-rich) thermal springs: Diversity and biotechnological analysis

Deciphering the geochemical influences on bacterial diversity and communities among two Algerian hot springs

Northeastern Algeria boasts numerous hot springs, yet these hydrothermal sites remain largely unexplored for their microbial ecology. The present study explores the bacterial abundance and diversity within two distinct Algerian hot springs (Hammam Saïda and Hammam Debagh) and investigates the link between the prevailing bacteria with geochemical parameters. High-throughput 16S rRNA gene sequencing of water and sediment samples revealed a bacterial dominance of 99.85-91.16% compared to Archaea (0.14-0.66%) in both springs. Interestingly, Saïda hot spring, characterized by higher temperatures and sodium content, harbored a community dominated by Pseudomonadota (51.13%), whereas Debagh, a Ca-Cl-SO4 type spring, was primarily populated by Bacillota with 55.33%. Bacteroidota displayed even distribution across both sites. Additional phyla, including Chloroflexota, Deinococcota, Cyanobacteriota, and Chlorobiota, were also present. Environmental factors, particularly temperature, sodium, potassium, and alkalinity, significantly influenced bacterial diversity and composition. These findings shed light on the interplay between distinct microbial communities and their associated geochemical properties, providing valuable insights for future research on biogeochemical processes in these unique ecosystems driven by distinct environmental conditions, including potential applications in bioremediation and enzyme discovery.

Characterization and identification of long-chain hydrocarbon-degrading bacterial communities in long-term chronically polluted soil in Ogoniland: an integrated approach using culture-dependent and independent methods

Escalating oil consumption has resulted in an increase in accidental spills of petroleum hydrocarbons, causing severe environmental degradation, notably in vulnerable regions like the Niger Delta. Complex mixture of these hydrocarbons particularly long-chain alkanes presents unique challenges in restoration of polluted environment due to their chemical properties. This study aimed to investigate the long-chain hydrocarbon-degrading bacterial communities within long-term chronically polluted soil in Ogoniland, by utilizing both traditional cultivation methods and modern culture-independent techniques. Results revealed that surface-polluted soil (SPS) and subsurface soil (SPSS) exhibit significantly higher total organic carbon (TOC) ranging from 5.64 to 5.06% and total petroleum hydrocarbons (TPH) levels ranging from 36,775 ppm to 14,087 ppm, compared to unpolluted soil (UPS) with 1.97% TOC and 479 ppm TPH, respectively. Analysis of carbon chain lengths reveals the prevalence of longer-chain alkanes (C20-28) in the surface soil. Culture-dependent methods, utilizing crude oil enrichment (COE) and paraffin wax enrichment (PWE), yield 47 bacterial isolates subjected to a long-chain alkane degradation assay. Twelve bacterial strains demonstrate significant degradation abilities across all enriched media. Three bacterial members, namely Pseudomonas sp. (almA), Marinomonas sp. (almA), and Alteromonas (ladA), exhibit genes responsible for long-chain alkane degradation, demonstrating efficiency between 50 and 80%. Culture-independent analysis reveals that surface SPS samples exhibit greater species richness and diversity compared to subsurface SPSS samples. Proteobacteria dominates as the phylum in both soil sample types, ranging from 22.23 to 82.61%, with Firmicutes (0.2-2.22%), Actinobacteria (0.4-3.02%), and Acidobacteria (0.1-3.53%) also prevalent. Bacterial profiles at genus level revealed that distinct variations among bacterial populations between SPS and SPSS samples comprising number of hydrocarbon degraders and the functional predictions also highlight the presence of potential catabolic genes (nahAa, adh2, and cpnA) in the polluted soil. However, culture-dependent analysis only captured a few of the dominant members found in culture-independent analysis, implying that more specialized media or environments are needed to isolate more bacterial members. The findings from this study contribute valuable information to ecological and biotechnological aspects, aiding in the development of more effective bioremediation applications for restoring oil-contaminated environments.

Metabolomics and Microbiomics Insights into Differential Surface Fouling of Three Macroalgal Species of Fucus (Fucales, Phaeophyceae) That Co-Exist in the German Baltic Sea

The brown algal genus Fucus provides essential ecosystem services crucial for marine environments. Macroalgae (seaweeds) release dissolved organic matter, hence, are under strong settlement pressure from micro- and macrofoulers. Seaweeds are able to control surface epibionts directly by releasing antimicrobial compounds onto their surfaces, and indirectly by recruiting beneficial microorganisms that produce antimicrobial/antifouling metabolites. In the Kiel Fjord, in the German Baltic Sea, three distinct Fucus species coexist: F. vesiculosus, F. serratus, and F. distichus subsp. evanescens. Despite sharing the same habitat, they show varying fouling levels; F. distichus subsp. evanescens is the least fouled, while F. vesiculosus is the most fouled. The present study explored the surface metabolomes and epiphytic microbiota of these three Fucus spp., aiming to uncover the factors that contribute to the differences in the fouling intensity on their surfaces. Towards this aim, algal surface metabolomes were analyzed using comparative untargeted LC-MS/MS-based metabolomics, to identify the marker metabolites influencing surface fouling. Their epiphytic microbial communities were also comparatively characterized using high-throughput amplicon sequencing, to pinpoint the differences in the surface microbiomes of the algae. Our results show that the surface of the least fouling species, F. distichus subsp. evanescens, is enriched with bioactive compounds, such as betaine lipids MGTA, 4-pyridoxic acid, and ulvaline, which are absent from the other species. Additionally, it exhibits a high abundance of the fungal genera Mucor and Alternaria, along with the bacterial genus Yoonia-Loktanella. These taxa are known for producing antimicrobial/antifouling compounds, suggesting their potential role in the observed fouling resistance on the surface of the F. distichus subsp. evanescens compared to F. serratus and F. vesiculosus. These findings provide valuable clues on the differential surface fouling intensity of Fucus spp., and their importance in marine chemical defense and fouling dynamics.

Evaluating the microcystin-LR-degrading potential of bacteria growing in extreme and polluted environments

Inhabitants of extreme and polluted environments are attractive as candidates for environmental bioremediation. Bacteria growing in oil refinery effluents, tannery dumpsite soils, car wash effluents, salt pans and hot springs were screened for microcystin-LR biodegradation potentials. Using a colorimetric BIOLOG MT2 assay; Arthrobacter sp. B105, Arthrobacter junii, Plantibacter sp. PDD-56b-14, Acinetobacter sp. DUT-2, Salinivibrio sp. YH4, Bacillus sp., Bacillus thuringiensis and Lysinibacillus boronitolerans could grow in the presence of microcystin-LR at 1, 10 and 100 µg L^-1. Most bacteria grew optimally at 10 µg L^-1 microcystin-LR under alkaline pH (8 and 9). The ability of these bacteria to use MC-LR as a growth substrate depicts their ability to metabolize the toxin, which is equivalent to its degradation. Through PCR screening, these bacteria were shown to lack the mlr genes implying possible use of a unique microcystin-LR degradation pathway. The study highlights the wide environmental and taxonomic distribution of microcystin-LR degraders.

Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel

The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.

Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India

Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.

Physico-Chemical and Metagenomic Profile Analyses of Animal Manures Routinely Used as Inocula in Anaerobic Digestion for Biogas Production

Anaerobic digestion (AD) of organic waste is considered a sustainable solution to energy shortage and waste management challenges. The process is facilitated by complex communities of micro-organisms, yet most wastes do not have these and thus need microbial inoculation using animal manures to initiate the process. However, the degradation efficiency and methane yield achieved in using different inocula vary due to their different microbial diversities. This study used metagenomics tools to compare the autochthonous microbial composition of cow, pig, chicken, and horse manures commonly used for biogas production. Cows exhibited the highest carbon utilisation (>30%) and showed a carbon to nitrogen ratio (C/N) favourable for microbial growth. Pigs showed the least nitrogen utilisation (<3%) which explains their low C/N whilst horses showed the highest nitrogen utilisation (>40%), which explains its high C/N above the optimal range of 20−30 for efficient AD. Manures from animals with similar gastrointestinal tract (GIT) physiologies were observed to largely harbour similar microbial communities. Conversely, some samples from animals with different GITs also shared common microbial communities plausibly because of similar diets and rearing conditions. Insights from this study will lay a foundation upon which in-depth studies of AD metabolic pathways and strategies to boost methane production through efficient catalysis can be derived.

Composition and Functional Diversity of Epiphytic Bacterial and Fungal Communities on Marine Macrophytes in an Intertidal Zone

Marine macrophytes (seagrasses and macroalgae) and their epiphytic microorganisms play an important role in the ecological and biochemical processes of coastal oceans. However, simultaneous comparative studies on the biodiversity and functions of epiphytic bacteria and fungi associated with marine macrophytes have not been conducted. In this study, high-throughput sequencing technology was used to describe the epiphytic bacterial and fungal communities of 11 common macroalgae and 2 seagrasses from an intertidal zone of northern China and compare them with seawater communities. The results showed that Proteobacteria and Bacteroidota were the dominant bacterial phyla in marine macrophytes, whereas Ascomycota, Chytridiomycota, and Basidiomycota were the dominant fungal phyla. The alpha diversity of the bacterial and fungal communities in seagrasses was the highest of all macrophyte samples. This may have been related to their ability to recruit microorganisms from multiple sources. Host phylogeny may influence bacterial community structure, and geographical differences may influence fungal community structure. The FAPROTAX data indicated that C metabolic microbes were enriched in marine macrophytes, while the FUNGuild data indicated that undefined saprotroph, which participated in organic matter degradation, were also enriched in marine macrophytes. These findings provide a theoretical basis regarding the epiphytic microorganisms of macrophytes and may offer new insights to support the improved ecological restoration of seagrass and macroalgae beds.

Comparative Metagenomic Analysis of Two Hot Springs From Ourense (Northwestern Spain) and Others Worldwide

With their circumneutral pH and their moderate temperature (66 and 68°C, respectively), As Burgas and Muiño da Veiga are two important human-use hot springs, previously studied with traditional culture methods, but never explored with a metagenomic approach. In the present study, we have performed metagenomic sequence-based analyses to compare the taxonomic composition and functional potential of these hot springs. Proteobacteria, Deinococcus-Thermus, Firmicutes, Nitrospirae, and Aquificae are the dominant phyla in both geothermal springs, but there is a significant difference in the abundance of these phyla between As Burgas and Muiño da Veiga. Phylum Proteobacteria dominates As Burgas ecosystem while Aquificae is the most abundant phylum in Muiño da Veiga. Taxonomic and functional analyses reveal that the variability in water geochemistry might be shaping the differences in the microbial communities inhabiting these geothermal springs. The content in organic compounds of As Burgas water promotes the presence of heterotrophic populations of the genera Acidovorax and Thermus, whereas the sulfate-rich water of Muiño da Veiga favors the co-dominance of genera Sulfurihydrogenibium and Thermodesulfovibrio. Differences in ammonia concentration exert a selective pressure toward the growth of nitrogen-fixing bacteria such as Thermodesulfovibrio in Muiño da Veiga. Temperature and pH are two important factors shaping hot springs microbial communities as was determined by comparative analysis with other thermal springs.

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.

Metagenomics revealing molecular profiling of community structure and metabolic pathways in natural hot springs of the Sikkim Himalaya

BACKGROUND

Himalaya is an ecologically pristine environment. The geo-tectonic activities have shaped various environmental niches with diverse microbial populations throughout the Himalayan biosphere region. Albeit, limited information is available in terms of molecular insights into the microbiome, including the uncultured microbes, of the Himalayan habitat. Hence, a vast majority of genomic resources are still under-explored from this region. Metagenome analysis has simplified the extensive in-depth exploration of diverse habitats. In the present study, the culture-independent whole metagenome sequencing methodology was employed for microbial diversity exploration and identification of genes involved in various metabolic pathways in two geothermal springs located at different altitudes in the Sikkim Himalaya.

RESULTS

The two hot springs, Polok and Reshi, have distinct abiotic conditions. The average temperature of Polok and Reshi was recorded to be 62 °C and 43 °C, respectively. Both the aquatic habitats have alkaline geochemistry with pH in the range of 7-8. Community profile analysis revealed genomic evidence of plentiful bacteria, with a minute fraction of the archaeal population in hot water reservoirs of Polok and Reshi hot spring. Mesophilic microbes belonging to Proteobacteria and Firmicutes phyla were predominant at both the sites. Polok exhibited an extravagant representation of Chloroflexi, Deinococcus-Thermus, Aquificae, and Thermotogae. Metabolic potential analysis depicted orthologous genes associated with sulfur, nitrogen, and methane metabolism, contributed by the microflora in the hydrothermal system. The genomic information of many novel carbohydrate-transforming enzymes was deciphered in the metagenomic description. Further, the genomic capacity of antimicrobial biomolecules and antibiotic resistance were discerned.

CONCLUSION

The study provided comprehensive molecular information about the microbial treasury as well as the metabolic features of the two geothermal sites. The thermal aquatic niches were found a potential bioresource of biocatalyst systems for biomass-processing. Overall, this study provides the whole metagenome based insights into the taxonomic and functional profiles of Polok and Reshi hot springs of the Sikkim Himalaya. The study generated a wealth of genomic data that can be explored for the discovery and characterization of novel genes encoding proteins of industrial importance.

Profiling Bacterial Diversity and Potential Pathogens in Wastewater Treatment Plants Using High-Throughput Sequencing Analysis

Next-generation sequencing provides new insights into the diversity and structure of bacterial communities, as well as the fate of pathogens in wastewater treatment systems. In this study, the bacterial community structure and the presence of pathogenic bacteria in three wastewater treatment plants across Gauteng province in South Africa were studied. The physicochemical results indicated that the quality of wastewater varies considerably from one plant to the others. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla across the three wastewater treatment plants, while Alphaproteobacteria, Actinobacteria, Bacilli, and Clostridia were the dominant classes. The dominant bacterial functions were highly associated with carbohydrate, energy, and amino acid metabolism. In addition, potential pathogenic bacterial members identified from the influent/effluent samples included Roseomonas, Bacillus, Pseudomonas, Clostridium, Mycobacterium, Methylobacterium, and Aeromonas. The results of linear discriminant analysis (LDA) effect size analysis also confirmed that these bacterial pathogens were significantly abundant in the wastewater treatment systems. Further, the results of this study highlighted that the presence of bacterial pathogens in treated effluent pose a potential contamination risk, transmitted through soil, agriculture, water, or sediments. There is thus a need for continuous monitoring of potential pathogens in wastewater treatment plants (WWTPs) in order to minimize public health risk.

Eukaryotic organisms of continental hydrothermal systems

Continental hydrothermal systems are a dynamic component of global thermal and geochemical cycles, exerting a pronounced impact on water chemistry and heat storage. As such, these environments are commonly classified by temperature, thermal fluid ionic concentration, and pH. Terrestrial hydrothermal systems are a refuge for extremophilic organisms, as extremes in temperature, metal concentration, and pH profoundly impact microorganism assemblage composition. While numerous studies focus on Bacteria and Archaea in these environments, few focus on Eukarya-likely due to lower temperature tolerances and because they are not model organisms for understanding the evolution of early life. However, where present, eukaryotic organisms are significant members of continental hydrothermal microorganism communities. Thus, this manuscript focuses on the eukaryotic occupants of terrestrial hydrothermal systems and provides a review of the current status of research, including microbe-eukaryote interactions and suggestions for future directions.

Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes

There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.

Thermophilic bacterial communities inhabiting the microbial mats of "indifferent" and chalybeate (iron-rich) thermal springs: Diversity and biotechnological analysis

Microbial mats are occasionally reported in thermal springs and information on such mats is very scarce. In this study, microbial mats were collected from two hot springs (Brandvlei (BV) and Calitzdorp (CA)), South Africa and subjected to scanning electron microscopy (SEM) and targeted 16S rRNA gene amplicon analysis using Next Generation Sequencing (NGS). Spring water temperature was 55°C for Brandvlei and 58°C for Calitzdorp while the pH of both springs was slightly acidic, with an almost identical pH range (6.2-6.3). NGS analysis resulted in a total of 4943 reads, 517 and 736 OTUs for BV and CA at, respectively, a combined total of 14 different phyla in both samples, 88 genera in CA compared to 45 in BV and 37.64% unclassified sequences in CA compared to 27.32% recorded in BV. Dominant bacterial genera in CA microbial mat were Proteobacteria (29.19%), Bacteroidetes (9.41%), Firmicutes (9.01%), Cyanobacteria (6.89%), Actinobacteria (2.65%), Deinococcus-Thermus (2.57%), and Planctomycetes (1.94%) while the BV microbial mat was dominated by Bacteroidetes (47.3%), Deinococcus-Thermus (12.35%), Proteobacteria (7.98%), and Planctomycetes (2.97%). Scanning electron microscopy results showed the presence of microbial filaments possibly resembling cyanobacteria, coccids, rod-shaped bacteria and diatoms in both microbial mats. Dominant genera that were detected in this study have been linked to different biotechnological applications including hydrocarbon degradation, glycerol fermentation, anoxic-fermentation, dehalogenation, and biomining processes. Overall, the results of this study exhibited thermophilic bacterial community structures with high diversity in microbial mats, which have a potential for biotechnological exploitation.