Denitrification in Great Basin hot springs

Hydrogen has been proposed to fuel primary production in the Aquificae dominated hot springs of Yellowstone National Park (Spear, et al. 2005), a finding the authors generalized to all hot springs. However, clone libraries derived from Great Basin springs contain few 16S ribosomal RNA (rRNA) gene sequences from Aquificae and many from unknown microorganisms. In the same springs, alternative electron donors rival the reducing power of hydrogen. This project will try to cultivate the uncharacterized microbes of two Great Basin springs and determine which electron donors they can use. Nitrogen is key to life. In its reduced form, ammonia, it is a primary constituent of nucleic acids and proteins. In its oxidized form,nitrate, it frequently substitutes for oxygen in anoxic conditions as microbes’ preferred electron acceptor for respiration. In this capacity, it drives energy capture–typically, though not always, in the process of denitrification [8]. Understanding the supply, demand, and interconversion of nitrogen through an ecosystem is essential to understanding the life within it. Although denitrification has been predicted to occur within hot springs on thermodynamic grounds, and some thermophilic isolates reduce nitrate, denitrification has never been examined in a hot spring. The hot springs of the Great Basin are under studied reservoirs of novel metabolisms and microbes, and are well worth in-depth exploration. Our project adapts techniques regularly used in marine and soil microbiology [6,7,9] to higher temperatures to test our hypothesis: that some thermophiles with in the hot springs respirenitrate, in the process of denitrification, for a significant amount of energy capture

Biogeography and Phylogeny of Aigarchaeota, A Novel Phylum of Archaea

‘Aigarchaeota’ is a candidate phylum of Archaea known only by 16S rRNA gene fragments from cultiva­tion-independent microbial surveys and a single composite genome from Candidatus ‘Caldiarchaeum sub­terraneum’, an inhabitant of a subterranean gold mine in Japan. Gene sequences associated with ‘Aigarchaeo­ta’ have been found in a variety of geothermal habits, however a comprehensive analysis of the phylogeny and distribution of ‘Aigarchaeota’ has not yet been done. Public databases were mined for 16S rRNA gene sequences related to known ‘Aigarchaeota’ and a combination of approaches were used to rigorously define the phylogenetic boundaries of the phylum, investigate its distribution, and design potential ‘Aigarchaeota’- specific primers. Approximately 300 16S rRNA genes and gene fragments affiliated with ‘Aigarchaeota’ were identified, phylogenic analyses suggested that ‘Aigarchaeota’ belonged to at least three family- to order-level groups and at least 13 genus-level groups, and supported the proposed relationship between ‘Aigarchaeota’, Thaumarchaeota, Crenarchaeota, and Korarchaeota in the so-called ‘TACK’ superphylum. A global distri­bution was suggested with genus-level group habitat differentiation. Some groups were predominantly ter­restrial (1A, 2B, 3, 4 & 5) while other groups were mostly found in Marine habitats (6-8). Fifteen strong ‘Ai­garchaeota’-specific primer candidates for the polymerase chain reaction (PCR) amplification of 16S rRNA genes were designed for further analyses

Microbial Endemism and Biogeography

The topic of microbial biogeography is almost 100 years old, however, when confronted with questions about the existence and extent of endemism in the microbial world, many microbiologists respond with opinions and theoretical arguments rather than examples of well-conducted studies. We begin this chapter with an overview of this debate as it applies to free-living prokayotes in part because there are relatively few good microbial biogeography studies. Furthermore, the arguments help to frame microbial biogeography in the larger context of biodiversity in that if endemism is common, then many more species exist

Are Incomplete Denitrification Pathways a Common Trait in Thermus Species from Geothermal Springs in China?

Temperature has strong impacts on ecosystem function and biogeochemical cycles, particularly within extreme environments such as geothermal springs above 60 °C. The primary focus of this study was to investigate the denitrification pathways of Thermus (Bacteria) isolates from geothermal springs from Tengchong, China. This study tested the hypothesis that incomplete denitrification is a common characteristic of the genus Thermus, regardless of geographic origin or species affiliation, which would implicate them in the efflux of nitrous oxide (a strong greenhouse gas) to the atmosphere. In this study, we cultivated 25 isolates, including six known Thermus species, and measured the stoichiometry of nitrogenous products of nitrate respiration using gas chromatography and colorimetric assays. We also designed custom primers for polymerase chain reaction (PCR) amplification of denitrification genes including narG, nirS, nirK, and norB to screen for the genetic capacity for each step in denitrification. Experimental results show that all Thermus strains tested display incomplete denitrification pathways terminating at nitrite (NO2 -) or nitrous oxide (N2O), and possibly nitric oxide (NO)

Microbial Nitrogen cycling in Nevada Geothermal Springs

Hot spring habitats above maximum photosynthetic temperature (73 ºC) are not well understood with respect to nitrogen (N) cycling. Few predictions have been made, and even fewer measurements of in situ activities have been reported. Thermodynamic calculations based on in situ chemical and temperature measurements will be used to predict the occurrence of the specific N-cycling reactions. In addition, these measurements in two springs will aid in an attempt to cultivate ammonia oxidizing species

Survey of Glycerol Dialkyl Glycerol Tetraethers (GDGTs) in Nevada and California Hot Springs and Selected T thermophiles

Glycerol dialkyl glycerol tetraethers (GDGTs) are core membrane lipids of many Archaea and some Bacteria found ubiquitously in soils and in many aqueous environments. Here, we examined the GDGT concentration in forty sediment samples from geothermal hot springs in the Great Basin (USA). Sediment samples were collected in tandem with extensive geochemical and site characterization. Hot spring temperatures ranged from 31 to 95°C and pH values from 6.8 to 10.7. Parametric Pearson\u27s correlation coefficients and nonparametric Spearman\u27s rho values were calculated to identify significant correlations between GDGT profiles and geochemical analytes. Isoprenoidal GDGTs (iGDGTs) negatively correlated with pH and positively correlated with temperature, Cr, and Cu, which is consistent with the importance of iGDGTs in the maintenance of membrane integrity at high temperature spring sources. In contrast, branched GDGTs (bGDGTs) displayed a negative relationship with temperature and a positive correlation with nitrate, nitrite and dissolved oxygen, demonstrating a niche for bGDGT-producing organisms in cooler, more oxidized springs away from the hottest geothermal sources. In addition, a collection of eleven thermophilic bacterial strains hypothesized to synthesize bGDGTs were tested; however, none synthesized GDGTs under the tested conditions. Our data provides insight into the environmental conditions under which archaeal and bacterial GDGTs are produced, which may improve the use of GDGTs as environmental proxies for understanding climates and conditions of the past and the future

Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea

To facilitate global efforts in addressing fundamental questions related to the biology of archaea, an international consortium of experts organized the International Workshop on Geo-Omics of Archaea (IWGOA), with the overarching themes of Ecology/Biogeochemistry, Metabolism, and Evolution. The IWGOA was held in Shenzhen, China, from October 25th to 27th, 2019. The meeting was attended by more than 200 attendees from China, Japan, USA, Australia, Germany, and France. Some of the most exciting oral and poster presentations made at the IWGOA are celebrated in this Research Topic Figure 1. The 21 manuscripts herein span different aspects of archaeal biology in both extreme and “non-extreme” environments in both marine and terrestrial settings and use a variety of approaches—community ecology, environmental lipidomics and genomics, organismal biology, and nucleic acid biochemistry—embodying diverse research thrusts that makes archaeal biology so exciting. At the same time, the manuscripts include over 100 authors from Asia, North America, and Europe, realizing our goal to engage a global audience in the biology of archaea

Novel thermophilic cellulolytic isolates belonging to the phylum Chloroflexi

Current biofuel technologies utilize valuable foodstuffs, such as corn kernels and cane sugar, as sources of easily metabolized sugars. Microbes are used to ferment these sugars into bioethanol, a first-generation biofuel. However, in order to avoid diverting foodstuffs from the food supply, the development of second-generation biofuels technology is necessary. Second-generation biofuels are produced by converting structurally complex lignocellulosic biomass, such as agricultural and municipal wastes, to fermentable sugars or directly to biofuels. The major technological hurdle limiting the mass production of second-generation biofuels is the difficulty in efficiently converting structurally complex lignocellulosic materials to fermentable sugars or directly to biofuels. The discovery of novel thermophilic microorganisms and enzymes that have high activities or broad substrate ranges on plant polymers addresses this challenge

Exploring diversity of Nitrate reducing thermophiles in Nevada hot springs

High rates of denitrification have been measured in Nevada geothermal hot springs, but little is known about the thermophiles that contribute to this activity. We hypothesize that heterotrophic bacteria in the genus Thermus are the most important denitrifiers in the springs. Alternatively, other microorganisms including chemolithotrophs may also be important. To test these hypotheses, several different strategies will be used to try to enrich and isolate nitrate-reducing microorganisms. Isolates will be identified by 16S rRNA gene PCR and sequencing. Subsequently, representative isolates will be chosen for nitrate reductase gene (narG) sequencing and for studies on the kinetics of nitrate reduction at high temperature. These data will provide information on how these microorganisms may behave in situ and how their activities may affect nitrogen cycling in the hot springs

A Spatial and temporal analysis of microbial communities in Great Boiling Spring, Nevada, U.S.A.

Great Boiling Spring (GBS) is a large, circumneutral, long residence time geothermal spring in the US Great Basin. Twelve samples were taken from four different sediment sites and the planktonic community in the bulk water of GBS on up to four different dates. Microbial community composition and diversity was assessed by using a barcoded, improved universal primer set targeting the V8 portion of the 16S rRNA gene and PCR. Over 200,000 products were sequenced using the Roche 454 GS FLX Titanium System. Sediment and planktonic microbial communities were distinct with very little overlap, regardless of the sampling location or temperature. Planktonic communities were extremely uneven and were dominated by a single phylotype related to Thermocrinis in the Aquificales. Benthic microbial communities grouped according to temperature and sampling location. Two locations, Site A (80-87°C) and Site B (79°C), were predominantly composed of the crenarchaeal class Thermoprotei, the novel archaeal lineage pSL4, and the novel bacterial lineage GAL35. Populations of the ammonia oxidizing archaeon “Candidatus Nitrosocaldus yellowstonii” comprised 5-15% of all samples when Site A was cooler than normal (80°C) and at cooler sites throughout the spring (76-62°C). At cooler temperature sites (76-62°C), the phylum-level diversity and evenness were significantly higher, and bacteria made up a significantly higher percentage of the population. To our knowledge, this is the most detailed study of the spatial and temporal variation in any geothermal spring. The study underscores the distinctness of planktonic and benthic communities and the importance of temperature in driving the spatial variation of microbial phylotypes throughout the mineralogically homogenous source pool. 8