scholarly journals Extremophilic Exopolysaccharides: Biotechnologies and Wastewater Remediation

2021 ◽  
Vol 12 ◽  
Author(s):  
Aparna Banerjee ◽  
Shrabana Sarkar ◽  
Tanvi Govil ◽  
Patricio González-Faune ◽  
Gustavo Cabrera-Barjas ◽  
...  
Keyword(s):  
Hydrothermal Vents ◽  
Hot Springs ◽  
Mine Drainage ◽  
Oil Spills ◽  
Extreme Environments ◽  
Substantial Part ◽  
Wastewater Remediation ◽  
Water Contaminants ◽  
Chemical Groups ◽  
Trace And Toxic Metals

Various microorganisms thrive under extreme environments, like hot springs, hydrothermal vents, deep marine ecosystems, hyperacid lakes, acid mine drainage, high UV exposure, and more. To survive against the deleterious effect of these extreme circumstances, they form a network of biofilm where exopolysaccharides (EPSs) comprise a substantial part. The EPSs are often polyanionic due to different functional groups in their structural backbone, including uronic acids, sulfated units, and phosphate groups. Altogether, these chemical groups provide EPSs with a negative charge allowing them to (a) act as ligands toward dissolved cations as well as trace, and toxic metals; (b) be tolerant to the presence of salts, surfactants, and alpha-hydroxyl acids; and (c) interface the solubilization of hydrocarbons. Owing to their unique structural and functional characteristics, EPSs are anticipated to be utilized industrially to remediation of metals, crude oil, and hydrocarbons from contaminated wastewaters, mines, and oil spills. The biotechnological advantages of extremophilic EPSs are more diverse than traditional biopolymers. The present review aims at discussing the mechanisms and strategies for using EPSs from extremophiles in industries and environment bioremediation. Additionally, the potential of EPSs as fascinating biomaterials to mediate biogenic nanoparticles synthesis and treat multicomponent water contaminants is discussed.

scholarly journals Habitat generalists or specialists, insights from comparative genomic analyses of Thermosipho lineages

2017 ◽  
Author(s):  
Thomas H.A. Haverkamp ◽  
Claire Geslin ◽  
Julien Lossouarn ◽  
Olga A. Podosokorskaya ◽  
Ilya Kublanov ◽  
...  
Keyword(s):  
Hydrothermal Vents ◽  
Hot Springs ◽  
Extreme Environments ◽  
Petroleum Reservoirs ◽  
Comparative Genomic ◽  
Mobile Dna ◽  
Genomic Analyses ◽  
Habitat Differentiation ◽  
Terrestrial Hot Springs ◽  
Habitat Generalists

AbstractThermosipho species inhabit various extreme environments such as marine hydrothermal vents, petroleum reservoirs and terrestrial hot springs. A 16S rRNA phylogeny of available Thermosipho spp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents and hotsprings. Comparative genomics and recombination analysis of the genomes of 15 Thermosipho isolates separated them into three species with different habitat distributions, the widely distributed T. africanus and the more specialized, T. melanesiensis and T. affectus. The three Thermosipho species can also be differentiated on the basis of genome content. For instance the T. africanus genomes had the largest repertoire of carbohydrate metabolism, which could explain why these isolates were obtained from ecologically more divergent habitats. The three species also show different capacities for defense against foreign DNA. T. melanesiensis and T. africanus both had a complete RM system, while this was missing in T. affectus. These observations also correlated with Pacbio sequencing, which revealed a methylated T. melanesiensis BI431 genome, while no methylation was detected among two T. affectus isolates. All the genomes carry CRISPR arrays accompanied by more or less complete CRISPR-cas systems. Interestingly, some isolates of both T. melanesiensis and T. africanus carry integrated prophage elements, with spacers matching these in their CRISPR arrays. Taken together, the comparative genomic analyses of Thermosipho spp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA that is present in subsurface ecosystems.

Archaeal habitats — from the extreme to the ordinary

2006 ◽  
Vol 52 (2) ◽  
pp. 73-116 ◽  
Author(s):  
Bonnie Chaban ◽  
Sandy Y.M Ng ◽  
Ken F Jarrell
Keyword(s):  
Hydrothermal Vents ◽  
Hot Springs ◽  
Soda Lakes ◽  
Carbon Sources ◽  
Extreme Environments ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Extreme Halophiles ◽  
Uncultured Archaea

The domain Archaea represents a third line of evolutionary descent, separate from Bacteria and Eucarya. Initial studies seemed to limit archaea to various extreme environments. These included habitats at the extreme limits that allow life on earth, in terms of temperature, pH, salinity, and anaerobiosis, which were the homes to hyper thermo philes, extreme (thermo)acidophiles, extreme halophiles, and methanogens. Typical environments from which pure cultures of archaeal species have been isolated include hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes, sewage digesters, and the rumen. Within the past two decades, the use of molecular techniques, including PCR-based amplification of 16S rRNA genes, has allowed a culture-independent assessment of microbial diversity. Remarkably, such techniques have indicated a wide distribution of mostly uncultured archaea in normal habitats, such as ocean waters, lake waters, and soil. This review discusses organisms from the domain Archaea in the context of the environments where they have been isolated or detected. For organizational purposes, the domain has been separated into the traditional groups of methanogens, extreme halophiles, thermoacidophiles, and hyperthermophiles, as well as the uncultured archaea detected by molecular means. Where possible, we have correlated known energy-yielding reactions and carbon sources of the archaeal types with available data on potential carbon sources and electron donors and acceptors present in the environments. From the broad distribution, metabolic diversity, and sheer numbers of archaea in environments from the extreme to the ordinary, the roles that the Archaea play in the ecosystems have been grossly underestimated and are worthy of much greater scrutiny.Key words: Archaea, methanogen, extreme halophile, hyperthermophile, thermoacidophile, uncultured archaea, habitats.

scholarly journals Factoring Origin of Life Hypotheses into the Search for Life in the Solar System and Beyond

Life ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 52 ◽  
Author(s):  
Alex Longo ◽  
Bruce Damer
Keyword(s):  
Solar System ◽  
Hydrothermal Vents ◽  
Hot Springs ◽  
Planetary Science ◽  
Icy Moons ◽  
Alternative Hypotheses ◽  
Biochemical Mechanisms ◽  
Early Mars ◽  
Life On Earth ◽  
Detection Strategies

Two widely-cited alternative hypotheses propose geological localities and biochemical mechanisms for life’s origins. The first states that chemical energy available in submarine hydrothermal vents supported the formation of organic compounds and initiated primitive metabolic pathways which became incorporated in the earliest cells; the second proposes that protocells self-assembled from exogenous and geothermally-delivered monomers in freshwater hot springs. These alternative hypotheses are relevant to the fossil record of early life on Earth, and can be factored into the search for life elsewhere in the Solar System. This review summarizes the evidence supporting and challenging these hypotheses, and considers their implications for the search for life on various habitable worlds. It will discuss the relative probability that life could have emerged in environments on early Mars, on the icy moons of Jupiter and Saturn, and also the degree to which prebiotic chemistry could have advanced on Titan. These environments will be compared to ancient and modern terrestrial analogs to assess their habitability and biopreservation potential. Origins of life approaches can guide the biosignature detection strategies of the next generation of planetary science missions, which could in turn advance one or both of the leading alternative abiogenesis hypotheses.

scholarly journals Phylogenetically novel uncultured microbial cells dominate Earth microbiomes

2018 ◽  
Author(s):  
Karen G. Lloyd ◽  
Joshua Ladau ◽  
Andrew D. Steen ◽  
Junqi Yin ◽  
Lonnie Crosby
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hydrothermal Vents ◽  
Hot Springs ◽  
Laboratory Culture ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Microbial Cells ◽  
Taxonomic Groups

AbstractTo unequivocally determine a microbe’s physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically-novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been well-studied, their global abundances, or number of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly-available metagenome and metatranscriptome databases, which we show are largely free of the culture-bias present in primer-amplified 16S rRNA gene surveys, to their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundance of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, non-human hosts, snow and bioreactors (22-87% uncultured genera to classes and 0-64% uncultured phyla). The exceptions were human and human-associated environments which were dominated by cultured genera (45-97%). We estimate that uncultured genera and phyla could comprise 7.3 × 1029(81%) and 2.2 × 1029(25%) microbial cells, respectively. Uncultured phyla were over-represented in meta transcript omes relative to metagenomes (46-84% of sequences in a given environment), suggesting that they are viable, and possibly more active than cultured clades. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate non-human environments on Earth, and their undiscovered physiologies may matter for Earth systems.

A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota

2021 ◽  
Author(s):  
Yafei Chang ◽  
Qilian Fan ◽  
Jialin Hou ◽  
Yu Zhang ◽  
Jing Li
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Extreme Environments ◽  
Reference Database ◽  
False Discovery Rate Method ◽  
Analysis Strategy ◽  
Gene Database ◽  
And Function ◽  
Functional Profiles

Abstract Microorganisms in deep-sea hydrothermal vents provide valuable insights into life under extreme conditions. Mass spectrometry-based proteomics has been widely used to identify protein expression and function. However, the metaproteomic studies in deep-sea microbiota have been constrained largely by the low identification rates of protein or peptide. To improve the efficiency of metaproteomics for hydrothermal vent microbiota, we firstly constructed a microbial gene database (HVentDB) based on 117 public metagenomic samples from hydrothermal vents and proposed a metaproteomic analysis strategy, which takes the advantages of not only the sample-matched metagenome, but also the metagenomic information released publicly in the community of hydrothermal vents. A two-stage false discovery rate method was followed up to control the risk of false positive. By applying our community-supported strategy to a hydrothermal vent sediment sample, about twice as many peptides were identified when compared with the ways against the sample-matched metagenome or the public reference database. In addition, more enriched and explainable taxonomic and functional profiles were detected by the HVentDB-based approach exclusively, as well as many important proteins involved in methane, amino acid, sugar, glycan metabolism and DNA repair, etc. The new metaproteomic analysis strategy will enhance our understanding of microbiota, including their lifestyles and metabolic capabilities in extreme environments. The database HVentDB is freely accessible from http://lilab.life.sjtu.edu.cn:8080/HventDB/main.html.

scholarly journals Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature

2020 ◽  
Vol 8 (6) ◽  
pp. 906 ◽  
Author(s):  
Francisco L. Massello ◽  
Chia Sing Chan ◽  
Kok-Gan Chan ◽  
Kian Mau Goh ◽  
Edgardo Donati ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Metabolic Profile ◽  
Hot Springs ◽  
Meta Analysis ◽  
Extreme Environments ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Phylogenetic Distance ◽  
Microbial Profile ◽  
The World

The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three hot springs from Neuquén, Argentina, using high-throughput amplicon sequencing. We predicted a distinct metabolic profile in the acidic and the circumneutral samples, with the first ones being dominated by chemolithotrophs and the second ones by chemoheterotrophs. Then, we collected data of the microbial communities of hot springs around the world in an effort to comprehend the roles of pH and temperature as shaping factors. Interestingly, there was a covariation between both parameters and the phylogenetic distance between communities; however, neither of them could explain much of the microbial profile in an ordination model. Moreover, there was no correlation between alpha diversity and these parameters. Therefore, the microbial communities’ profile seemed to have complex shaping factors beyond pH and temperature. Lastly, we looked for taxa associated with different environmental conditions. Several such taxa were found. For example, Hydrogenobaculum was frequently present in acidic springs, as was the Sulfolobaceae family; on the other hand, Candidatus Hydrothermae phylum was strongly associated with circumneutral conditions. Interestingly, some singularities related to sites featuring certain taxa were also observed.

scholarly journals Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Liangzhi Li ◽  
Zhenghua Liu ◽  
Min Zhang ◽  
Delong Meng ◽  
Xueduan Liu ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Evolutionary History ◽  
Mine Drainage ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Ecological Functions ◽  
History Of

ABSTRACT Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium. In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium. Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions. IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.

scholarly journals Phycobiliproteins from extreme environments and their potential applications

2020 ◽  
Vol 71 (13) ◽  
pp. 3827-3842 ◽  
Author(s):  
Anton Puzorjov ◽  
Alistair J McCormick
Keyword(s):  
Hot Springs ◽  
Elevated Temperatures ◽  
Algal Species ◽  
Extreme Environments ◽  
Fundamental Understanding ◽  
Thermophilic Species ◽  
Red Algal ◽  
Potential Applications ◽  
Thermophilic Organisms ◽  
Photosynthetic Adaptation

Abstract The light-harvesting phycobilisome complex is an important component of photosynthesis in cyanobacteria and red algae. Phycobilisomes are composed of phycobiliproteins, including the blue phycobiliprotein phycocyanin, that are considered high-value products with applications in several industries. Remarkably, several cyanobacteria and red algal species retain the capacity to harvest light and photosynthesise under highly selective environments such as hot springs, and flourish in extremes of pH and elevated temperatures. These thermophilic organisms produce thermostable phycobiliproteins, which have superior qualities much needed for wider adoption of these natural pigment–proteins in the food, textile, and other industries. Here we review the available literature on the thermostability of phycobilisome components from thermophilic species and discuss how a better appreciation of phycobiliproteins from extreme environments will benefit our fundamental understanding of photosynthetic adaptation and could provide a sustainable resource for several industrial processes.

scholarly journals Graphene Oxide–ZnO Nanocomposites for Removal of Aluminum and Copper Ions from Acid Mine Drainage Wastewater

2020 ◽  
Vol 17 (18) ◽  
pp. 6911
Author(s):  
Carolina Rodríguez ◽  
Camila Tapia ◽  
Enzo Leiva-Aravena ◽  
Eduardo Leiva
Keyword(s):  
Heavy Metals ◽  
Graphene Oxide ◽  
Zno Nanoparticles ◽  
Mine Drainage ◽  
Copper Ions ◽  
Wastewater Remediation ◽  
Ph Adjustment ◽  
Removal Capacity ◽  
Acidic Waters ◽  
Maximum Removal

Adsorption technologies are a focus of interest for the removal of pollutants in water treatment systems. These removal methods offer several design, operation and efficiency advantages over other wastewater remediation technologies. Particularly, graphene oxide (GO) has attracted great attention due to its high surface area and its effectiveness in removing heavy metals. In this work, we study the functionalization of GO with zinc oxide nanoparticles (ZnO) to improve the removal capacity of aluminum (Al) and copper (Cu) in acidic waters. Experiments were performed at different pH conditions (with and without pH adjustment). In both cases, decorated GO (GO/ZnO) nanocomposites showed an improvement in the removal capacity compared with non-functionalized GO, even when the pH of zero charge (pHPZC) was higher for GO/ZnO (5.57) than for GO (3.98). In adsorption experiments without pH adjustment, the maximum removal capacities for Al and Cu were 29.1 mg/g and 45.5 mg/g, respectively. The maximum removal percentages of the studied cations (Al and Cu) were higher than 88%. Further, under more acidic conditions (pH 4), the maximum sorption capacities using GO/ZnO as adsorbent were 19.9 mg/g and 33.5 mg/g for Al and Cu, respectively. Moreover, the removal percentages reach 95.6% for Al and 92.9% for Cu. This shows that decoration with ZnO nanoparticles is a good option for improving the sorption capacity of GO for Cu removal and to a lesser extent for Al, even when the pH was not favorable in terms of electrostatic affinity for cations. These findings contribute to a better understanding of the potential and effectiveness of GO functionalization with ZnO nanoparticles to treat acidic waters contaminated with heavy metals and its applicability for wastewater remediation.

scholarly journals Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

2014 ◽  
Vol 80 (12) ◽  
pp. 3677-3686 ◽  
Author(s):  
Jun Liu ◽  
Zheng-Shuang Hua ◽  
Lin-Xing Chen ◽  
Jia-Liang Kuang ◽  
Sheng-Jin Li ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Community Composition ◽  
Environmental Conditions ◽  
Mine Tailings ◽  
Large Scale ◽  
Hot Springs ◽  
Mine Drainage ◽  
Rrna Gene ◽  
Content Type ◽  
Geochemical Parameters

ABSTRACTRecent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within theAlphaproteobacteria,Deltaproteobacteria, andFirmicuteswere attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.

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