Ecological dichotomies arise in microbial communities due to mixing of deep hydrothermal waters and atmospheric gas in a circumneutral hot spring.

Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating faster growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen ∼2.4 Gya. IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral to alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼ 2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs.

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Metagenomic, Metabolomic, and Functional Evaluation of Kimchi Broth Treated with Light-Emitting Diodes (LEDs)

Metabolites ◽

10.3390/metabo11080472 ◽

2021 ◽

Vol 11 (8) ◽

pp. 472

Author(s):

Yeong-Ji Oh ◽

Ye-Rin Park ◽

Jungil Hong ◽

Do-Yup Lee

Keyword(s):

Amplicon Sequencing ◽

Taxonomic Composition ◽

Metabolic Phenotype ◽

Rrna Gene ◽

Functional Evaluation ◽

Initial Condition ◽

Microbial Composition ◽

Light Emitting ◽

Blue Led ◽

Red Led

The light-emitting diode (LED) has been widely used in the food industry, and its application has been focused on microbial sterilization, specifically using blue-LED. The investigation has been recently extended to characterize the biotic and abiotic (photodynamic) effects of different wavelengths. Here, we investigated LED effects on kimchi fermentation. Kimchi broths were treated with three different colored-LEDs (red, green, and blue) or kept in the dark as a control. Multiomics was applied to evaluate the microbial taxonomic composition using 16S rRNA gene amplicon sequencing, and the metabolomic profiles were determined using liquid chromatography–Orbitrap mass spectrometry. Cell viability was tested to determine the potential cytotoxicity of the LED-treated kimchi broths. First, the amplicon sequencing data showed substantial changes in taxonomic composition at the family and genus levels according to incubation (initial condition vs. all other groups). The differences among the treated groups (red-LED (RLED), green-LED (GLED), blue-LED (BLED), and dark condition) were marginal. The relative abundance of Weissella was decreased in all treated groups compared to that of the initial condition, which coincided with the decreased composition of Lactobacillus. Compositional changes were relatively high in the GLED group. Subsequent metabolomic analysis indicated a unique metabolic phenotype instigated by different LED treatments, which led to the identification of the LED treatment-specific and common compounds (e.g., luteolin, 6-methylquinoline, 2-hydroxycinnamic acid, and 9-HODE). These results indicate that different LED wavelengths induce characteristic alterations in the microbial composition and metabolomic content, which may have applications in food processing and storage with the aim of improving nutritional quality and the safety of food.

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Contribution of Gammarus lacustris to phosphorus recycling in a fishless alpine lake

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f99-107 ◽

1999 ◽

Vol 56 (9) ◽

pp. 1679-1686 ◽

Cited By ~ 13

Author(s):

Frank M Wilhelm ◽

Jeff J Hudson ◽

David W Schindler

Keyword(s):

Water Column ◽

Vertical Migration ◽

Mountain Lakes ◽

Plankton Community ◽

Alpine Lake ◽

Gammarus Lacustris ◽

Benthic Pelagic Coupling ◽

Phosphorus Recycling ◽

Planktonic Community ◽

Total P

We estimated the net P transport by Gammarus lacustris from the benthic to pelagic regions of a fishless alpine lake and compared it with P regeneration by the entire plankton community. Gammarus lacustris released between 5.2 and 18.1 ng P·L-1·h-1 (adults only and adults plus immatures, respectively) in the pelagic region during nighttime vertical migration. Additional P released into and removed from the water column due to predation on zooplankton was estimated at 1.87 and 2.3 ng P·L-1·h-1, respectively. The net daily regeneration of 52.2-181.4 ng P·L-1·day-1 by the G. lacustris population represented 9.5-32.9% of the total P regenerated by the planktonic community. The majority of the P released by G. lacustris represents "new" P to the pelagic zone because it originated in sediments. We conclude that G. lacustris can represent an important link in benthic-pelagic coupling in oligotrophic mountain lakes.

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Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs

Microbiome ◽

10.1186/s40168-021-01090-1 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Chanenath Sriaporn ◽

Kathleen A. Campbell ◽

Martin J. Van Kranendonk ◽

Kim M. Handley

Keyword(s):

Hot Springs ◽

Hot Spring ◽

Thermal Adaptation ◽

Distinct Species ◽

Taupo Volcanic Zone ◽

Rrna Gene ◽

Ph Homeostasis ◽

Microbial Composition ◽

Related Group ◽

Geothermal Environments

Abstract Background Terrestrial hot spring settings span a broad spectrum of physicochemistries. Physicochemical parameters, such as pH and temperature, are key factors influencing differences in microbial composition across diverse geothermal areas. Nonetheless, analysis of hot spring pools from the Taupo Volcanic Zone (TVZ), New Zealand, revealed that some members of the bacterial genus, Acidithiobacillus, are prevalent across wide ranges of hot spring pHs and temperatures. To determine the genomic attributes of Acidithiobacillus that inhabit such diverse conditions, we assembled the genomes of 19 uncultivated hot spring Acidithiobacillus strains from six geothermal areas and compared these to 37 publicly available Acidithiobacillus genomes from various habitats. Results Analysis of 16S rRNA gene amplicons from 138 samples revealed that Acidithiobacillus comprised on average 11.4 ± 16.8% of hot spring prokaryotic communities, with three Acidithiobacillus amplicon sequence variants (ASVs) (TVZ_G1, TVZ_G2, TVZ_G3) accounting for > 90% of Acidithiobacillus in terms of relative abundance, and occurring in 126 out of 138 samples across wide ranges of temperature (17.5–92.9 °C) and pH (1.0–7.5). We recovered 19 environmental genomes belonging to each of these three ASVs, as well as a fourth related group (TVZ_G4). Based on genome average nucleotide identities, the four groups (TVZ_G1-TVZ_G4) constitute distinct species (ANI < 96.5%) of which three are novel Acidithiobacillus species (TVZ_G2-TVZ_G4) and one belongs to Acidithiobacillus caldus (TVZ_G1). All four TVZ Acidithiobacillus groups were found in hot springs with temperatures above the previously known limit for the genus (up to 40 °C higher), likely due to significantly higher proline and GC contents than other Acidithiobacillus species, which are known to increase thermostability. Results also indicate hot spring-associated Acidithiobacillus have undergone genome streamlining, likely due to thermal adaptation. Moreover, our data suggest that Acidithiobacillus prevalence across varied hot spring pHs is supported by distinct strategies, whereby TVZ_G2-TVZ_G4 regulate pH homeostasis mostly through Na+/H+ antiporters and proton-efflux ATPases, whereas TVZ_G1 mainly relies on amino acid decarboxylases. Conclusions This study provides insights into the distribution of Acidithiobacillus species across diverse hot spring physichochemistries and determines genomic features and adaptations that potentially enable Acidithiobacillus species to colonize a broad range of temperatures and pHs in geothermal environments.

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Fluids in Submarine Mid-Ocean Ridge Hydrothermal Settings

Elements ◽

10.2138/gselements.16.6.389 ◽

2020 ◽

Vol 16 (6) ◽

pp. 389-394

Author(s):

Esther M. Schwarzenbach ◽

Matthew Steele-MacInnis

Keyword(s):

Heat Budget ◽

Oceanic Lithosphere ◽

Life Forms ◽

Hydrothermal Systems ◽

Hydrothermal Fluids ◽

Early Earth ◽

Geologic Time ◽

Mid Ocean Ridge ◽

Time Changes ◽

Ocean Ridge

Seawater interaction with the oceanic lithosphere crucially impacts on global geochemical cycles, controls ocean chemistry over geologic time, changes the petrophysical properties of the oceanic lithosphere, and regulates the global heat budget. Extensive seawater circulation is expressed near oceanic ridges by the venting of hydrothermal fluids through chimney structures. These vent fluids vary greatly in chemistry, from the metal-rich, acidic fluids that emanate from “black smokers” at temperatures up to 400 °C to the metal-poor, highly alkaline and reducing fluids that issue from the carbonate–brucite chimneys of ultramafic-hosted systems at temperatures below 110 °C. Mid-ocean ridge hydrothermal systems not only generate signifi-cant metal resources but also host unique life forms that may be similar to those of early Earth.

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The Microbial Composition in Circumneutral Thermal Springs from Chignahuapan, Puebla, Mexico Reveals the Presence of Particular Sulfur-Oxidizing Bacterial and Viral Communities

Microorganisms ◽

10.3390/microorganisms8111677 ◽

2020 ◽

Vol 8 (11) ◽

pp. 1677

Author(s):

Hugo Gildardo Castelán-Sánchez ◽

Pablo M. Meza-Rodríguez ◽

Erika Carrillo ◽

David I. Ríos-Vázquez ◽

Arturo Liñan-Torres ◽

...

Keyword(s):

Hot Springs ◽

Hot Spring ◽

Sulfur Cycle ◽

Thermal Springs ◽

Microbial Composition ◽

Bacterial Populations ◽

Sulfur Oxidizing ◽

Specific Species ◽

Shotgun Approach ◽

Auxiliary Metabolic Genes

Terrestrial thermal springs are widely distributed globally, and these springs harbor a broad diversity of organisms of biotechnological interest. In Mexico, few studies exploring this kind of environment have been described. In this work, we explore the microbial community in Chignahuapan hot springs, which provides clues to understand these ecosystems’ diversity. We assessed the diversity of the microorganism communities in a hot spring environment with a metagenomic shotgun approach. Besides identifying similarities and differences with other ecosystems, we achieved a systematic comparison against 11 metagenomic samples from diverse localities. The Chignahuapan hot springs show a particular prevalence of sulfur-oxidizing bacteria from the genera Rhodococcus, Thermomonas, Thiomonas, Acinetobacter, Sulfurovum, and Bacillus, highlighting those that are different from other recovered bacterial populations in circumneutral hot springs environments around the world. The co-occurrence analysis of the bacteria and viruses in these environments revealed that within the Rhodococcus, Thiomonas, Thermonas, and Bacillus genera, the Chignahuapan samples have specific species of bacteria with a particular abundance, such as Rhodococcus erytropholis. The viruses in the circumneutral hot springs present bacteriophages within the order Caudovirales (Siphoviridae, Myoviridae, and Podoviridae), but the family of Herelleviridae was the most abundant in Chignahuapan samples. Furthermore, viral auxiliary metabolic genes were identified, many of which contribute mainly to the metabolism of cofactors and vitamins as well as carbohydrate metabolism. Nevertheless, the viruses and bacteria present in the circumneutral environments contribute to the sulfur cycle. This work represents an exhaustive characterization of a community structure in samples collected from hot springs in Mexico and opens opportunities to identify organisms of biotechnological interest.

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Hydrogen and Abiotic Hydrocarbons: Molecules that Change the World

Elements ◽

10.2138/gselements.16.1.13 ◽

2020 ◽

Vol 16 (1) ◽

pp. 13-18 ◽

Cited By ~ 1

Author(s):

Laurent Truche ◽

Thomas M. McCollom ◽

Isabelle Martinez

Keyword(s):

Molecular Hydrogen ◽

Hydrothermal Fluids ◽

Energy Resources ◽

Ultramafic Rocks ◽

Biological Communities ◽

Microbial Life ◽

The World ◽

The Subject ◽

Scientific Attention ◽

Deep Fractures

Molecular hydrogen (H2), methane, and hydrocarbons with an apparent abiotic origin have been observed in a variety of geologic settings, including serpentinized ultramafic rocks, hydrothermal fluids, and deep fractures within ancient cratons. Molecular hydrogen is also observed in vapor plumes emanating from the icy crust of Saturn’s moon Enceladus, and methane has been detected in the atmosphere of Mars. Geologic production of these compounds has been the subject of increasing scientific attention due to their use by chemosynthetic biological communities. These compounds are also of interest as possible energy resources. This issue summarizes the geological sources of abiotic H2 and hydrocarbons on Earth and elsewhere and examines their impact on microbial life and energy resources.

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Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity

mSphere ◽

10.1128/msphere.00626-18 ◽

2019 ◽

Vol 4 (1) ◽

Cited By ~ 5

Author(s):

Sarahi L. Garcia ◽

Anna J. Szekely ◽

Christoffer Bergvall ◽

Martha Schattenhofer ◽

Sari Peura

Keyword(s):

Climate Change ◽

Snow Cover ◽

Water Column ◽

Relative Abundance ◽

Heterotrophic Bacteria ◽

Methane Emissions ◽

Boreal Lakes ◽

Climate Change Scenarios ◽

Primary Producers ◽

Microbial Composition

ABSTRACT Climate change scenarios anticipate decreased spring snow cover in boreal and subarctic regions. Forest lakes are abundant in these regions and substantial contributors of methane emissions. To investigate the effect of reduced snow cover, we experimentally removed snow from an anoxic frozen lake. We observed that the removal of snow increased light penetration through the ice, increasing water temperature and modifying microbial composition in the different depths. Chlorophyll a and b concentrations increased in the upper water column, suggesting activation of algal primary producers. At the same time, Chlorobiaceae, one of the key photosynthetic bacterial families in anoxic lakes, shifted to lower depths. Moreover, a decrease in the relative abundance of methanotrophs within the bacterial family Methylococcaceae was detected, concurrent with an increase in methane concentration in the water column. These results indicate that decreased snow cover impacts both primary production and methane production and/or consumption, which may ultimately lead to increased methane emissions after spring ice off. IMPORTANCE Small lakes are an important source of greenhouse gases in the boreal zone. These lakes are severely impacted by the winter season, when ice and snow cover obstruct gas exchange between the lake and the atmosphere and diminish light availability in the water column. Currently, climate change is resulting in reduced spring snow cover. A short-term removal of the snow from the ice stimulated algal primary producers and subsequently heterotrophic bacteria. Concurrently, the relative abundance of methanotrophic bacteria decreased and methane concentrations increased. Our results increase the general knowledge of microbial life under ice and, specifically, the understanding of the potential impact of climate change on boreal lakes.

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Isotope geochemistry of gallium in hydrothermal systems

10.26686/wgtn.17020043.v1 ◽

2021 ◽

Author(s):

◽

Constance E. Payne

Keyword(s):

New Zealand ◽

Ion Exchange ◽

Column Chromatography ◽

Hot Spring ◽

Isotope Geochemistry ◽

Isotopic Ratio ◽

Hydrothermal Systems ◽

Phase Changes ◽

Hydrothermal Fluids ◽

Taupo Volcanic Zone

<p>Little is known about the isotope geochemistry of gallium in natural systems (Groot, 2009), with most information being limited to very early studies of gallium isotopes in extra-terrestrial samples (Aston, 1935; De Laeter, 1972; Inghram et al., 1948; Machlan et al., 1986). This study is designed as a reconnaissance for gallium isotope geochemistry in hydrothermal systems of New Zealand. Gallium has two stable isotopes, ⁶⁹Ga and ⁷¹Ga, and only one oxidation state, Ga³⁺, in aqueous media (Kloo et al., 2002). This means that fractionation of gallium isotopes should not be effected by redox reactions. Therefore the physical processes that occur during phase changes of hydrothermal fluids (i.e. flashing of fluids to vapour phase and residual liquid phase) and mineralisation of hydrothermal precipitates (i.e. precipitation and ligand exchange) can be followed by studying the isotopes of gallium. A gallium anomaly is known to be associated with some hydrothermal processes as shown by the unusual, elevated concentrations (e.g. 290 ppm in sulfide samples of Waiotapu; this study) in several of the active geothermal systems in New Zealand. The gallium isotope system has not yet been investigated since the revolution of high precision isotopic ratio measurements by Multi-Collector Inductively Coupled Plasma Mass Spectrometry (MC-ICPMS) and so a new analytical methodology needed to be established. Any isotopic analysis of multi-isotope elements must satisfy a number of requirements in order for results to be both reliable and meaningful. Most importantly, the analysis must represent the true isotopic composition of the sample. Ion-exchange chromatography is generally utilised to purify samples for analysis by MC-ICPMS and exclude potential mass interfering elements but care must also be taken to recover as close to 100% of the element of interest as possible, as column chromatography can often result in fractionation of isotopes (Albarède and Beard, 2004). An ion exchange column chromatography methodology for the separation of gallium based on earlier work by Strelow and associates (Strelow, 1980a, b; Strelow and van der Walt, 1987; Strelow et al., 1974; van der Walt and Strelow, 1983) has been developed to ensure a quantitative and clean separation from the majority of elements commonly associated with hydrothermal precipitates and waters (i.e. As, Sb, Mo, Hg, W, Tl, Fe and other transition metals). A protocol to measure the isotopes of Ga was developed by the adaptation of methods used for other stable isotope systems using the Nu Plasma MC-ICPMS at the School of Geography, Environment and Earth Sciences, Victoria University of Wellington, NZ. Gallium isotopic ratios have been collected for a suite of samples representing the migration of hydrothermal fluids from deep fluids in geothermal reservoirs to the surface expression of hot spring waters and associated precipitates in hydrothermal systems. A range in δ⁷¹GaSRM994 values is observed in samples from Taupo Volcanic Zone geothermal fields from -5.49‰ to +2.65‰ in silica sinter, sulfide, mud and brine samples. Mineral samples from Tsumeb and Kipushi mines range from -11.92‰ to +2.58‰ δ⁷¹GaSRM994. Two rock standards, BHVO-2 and JR-2 were also analysed for gallium isotopes with δ⁷¹GaSRM994 values of -0.92‰ ±0.12‰ and -1.91‰ ±0.23‰ respectively.</p>

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Distinct microbial composition and functions in an underground high-temperature hot spring at different depths

10.5194/bg-2019-406 ◽

2019 ◽

Cited By ~ 1

Author(s):

Shijie Bai ◽

Xiaotong Peng

Keyword(s):

High Temperature ◽

Microbial Communities ◽

Hot Springs ◽

Hot Spring ◽

Hydrogen Oxidation ◽

Archaeal Community ◽

Limited Area ◽

Rrna Gene ◽

Microbial Composition ◽

Different Depths

Abstract. The microbial diversity and functions of three high-temperature neutral hot springs water samples at different depths (0 m, 19 m and 58 m) were investigated based on 16S rRNA gene sequencing and a functional gene array (GeoChip 5.0). The results revealed that the bacterial communities were distinct at different depths in the hot springs. Additionally, in response to the depths, bacterial/archaeal community compositions exhibited shifts over the depth profiles. Aquificae, Alpha-proteobacteria, and Deinococcus-Thermus were the dominating phyla at 0 m, 19 m, and 58 m, respectively. Hydrogenobacter, Sphingobium, and Thermus were the most abundant genera at 0 m, 19 m, and 58 m, respectively. The phylum Thaumarchaeota was the most abundant member of the archaeal community in the samples at different hot spring depths. Functional results of the microbial communities indicated that microbial metabolic functions were mainly related to sulfur, nitrogen cycling, and hydrogen oxidation. In summary, our results demonstrated that distinct microbial communities and functions were found at different depths of hot springs in a very limited area. These findings will provide new insights into the deep-subsurface biosphere associated with terrestrial hot springs.

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Geochemical influences on nonenzymatic oligomerization of prebiotically relevant cyclic nucleotides

10.1101/872234 ◽

2019 ◽

Author(s):

Shikha Dagar ◽

Susovan Sarkar ◽

Sudha Rajamani

Keyword(s):

Cyclic Nucleotides ◽

Hot Spring ◽

Rna World ◽

Early Earth ◽

Pyrimidine Nucleotides ◽

Diurnal Cycles ◽

Alkaline Conditions ◽

Purine And Pyrimidine Nucleotides ◽

The Stability ◽

Emergence Of Life

AbstractThe spontaneous emergence of RNA on the early Earth continues to remain an enigma in the field of origins of life. Few studies have looked at the nonenzymatic oligomerization of cyclic nucleotides under neutral to alkaline conditions, in fully dehydrated state. Herein, we systematically investigated the oligomerization of cyclic nucleotides under prebiotically relevant conditions, where starting reactants were subjected to repeated dehydration-rehydration (DH-RH) regimes, like they would have been on an early Earth. DH-RH conditions, a recurring geological theme, are driven by naturally occurring processes including diurnal cycles and tidal pool activity. These conditions have been shown to facilitate uphill oligomerization reactions in terrestrial geothermal niches, which are hypothesized to be pertinent sites for the emergence of life. 2′-3′ and 3′-5′ cyclic nucleotides of one purine-based (adenosine) and one pyrimidine-based (cytidine) system were evaluated in this study. Additionally, the effect of amphiphiles was also investigated. Furthermore, to discern the effect of ‘realistic’ conditions on this process, the reactions were also performed using hot spring water samples from an early Earth analogue environment. Our results showed that the oligomerization of cyclic nucleotides under DH-RH conditions resulted in intact informational oligomers. Amphiphiles increased the stability of, both, the starting monomers and the resultant oligomers. In analogue condition reactions, oligomerization of nucleotides and back-hydrolysis of the resultant oligomers was pronounced. Altogether, this study demonstrates how nonenzymatic oligomerization of cyclic purine and pyrimidine nucleotides, under laboratory-simulated and early Earth analogous conditions, could have resulted in RNA oligomers of a putative RNA World.

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