Abstract Fungi are natural decomposers that degrade organic substrates for growth. On Earth, fungi grow and produce mushrooms on various natural substrates, often with little to no added nutrient supplements. Existing waste substrates found on board the International Space Station (ISS) such as inedible biomass from plants, clothing, and plastic wastes from prepackaged foods could be repurposed for food production and advance the capacity for more sustainable long-duration space missions. The sporeless oyster mushroom (Pleurotus ostreatus) strain SPX was grown on seven substrates in varied combination recipes to investigate how ISS waste streams could be used to cultivate mushrooms. In addition, food safety analyses were performed to assess the feasibility of mushroom cultivation as a low-risk food option. Results show that waste streams of cotton t-shirts and inedible biomass from plants are potential substrates that could support mushroom cultivation on board the ISS. By using materials that are already available on the station, the upmass needed to support such efforts is reduced and waste products can be recycled to potentially yield more food. This investigation was intended to identify the feasibility of incorporating mushrooms as a potential space crop without the requirement of a large upmass of substrates being brought to the ISS.

Alternaria alternata is a ubiquitous fungus and a major allergen associated with the development of asthma. Inhalation of intact spores is the primary cause of human exposure to fungal allergen. However, allergen-rich cultured fungal filtrates are oftentimes used in the current models of fungal sensitization that do not fully reflect real-life exposures. Thus, establishing novel spore exposure models is imperative. In this study, we established novel fungal exposure models of both adult and neonate to live spores. We examined pathophysiological changes in the spore models as compared to the non-exposure controls and also to the conventional filtrate models. While both Alternaria filtrate- and spore-exposed adult BALB/c mice developed elevated airway hyperresponsiveness (AHR), filtrates induced a greater IgE mediated response and higher broncholavage eosinophils than spores. In contrast, the mice exposed to Alternaria spores had higher numbers of neutrophils. Both exposures induced comparable levels of lung tissue inflammation and mucous cell metaplasia (MCM). In the neonatal model, exposure to Alternaria spores resulted in a significant increase of AHR in both adult and neonatal mice. Increased levels of IgE in both neonatal and adult mice exposed to spores was associated with increased eosinophilia in the treatment groups. Adult demonstrated increased numbers of lymphocytes that was paralleled by increased IgG1 production. Both adults and neonates demonstrated similarly increased eosinophilia, IgE, tissue inflammation and MCM.

The construction of optimized biological fuel cells requires a cathode which combines the longevity of a microbial catalyst with the current density of an enzymatic catalyst. Laccase-secreting fungi were grown directly on the cathode of a biological fuel cell to facilitate the exchange of inactive enzymes with active enzymes, with the goal of extending the lifetime of laccase cathodes. Directly incorporating the laccase-producing fungus at the cathode extends the operational lifetime of laccase cathodes while eliminating the need for frequent replenishment of the electrolyte. The hybrid microbial–enzymatic cathode addresses the issue of enzyme inactivation by using the natural ability of fungi to exchange inactive laccases at the cathode with active laccases. Finally, enzyme adsorption was increased through the use of a functionally graded coating containing an optimized ratio of titanium dioxide nanoparticles and single-walled carbon nanotubes. The hybrid microbial–enzymatic fuel cell combines the higher current density of enzymatic fuel cells with the longevity of microbial fuel cells, and demonstrates the feasibility of a self-regenerating fuel cell in which inactive laccases are continuously exchanged with active laccases.

Background and objective A novel fungal allergen, Alternaria (Alt), has been previously shown to associate with the pathogenesis of allergic rhinitis and bronchial asthma, particularly in arid and semi-arid regions. Airway epithelial cells are among the first to encounter Alt, and epithelial cytokine production and subsequent airway inflammation are early events in the response to Alt exposure. However, the underlying mechanism is unclear. As protease-activated receptor 2 (PAR2) has been implicated in most of the Alt-induced biological events, we investigated the regulation of airway inflammation and epithelial cytokine expression by PAR2. Methods Wild-type (WT) and Par2 knockout (Par2-KO) mice were used to evaluate the in vivo role of PAR2. Primary human and mouse airway epithelial cells were used to examine the mechanistic basis of epithelial cytokine regulation in vitro. Results Surprisingly, Par2 deficiency had no negative impact on the change of lung function, inflammation and cytokine production in the mouse model of Alt-induced asthma. Alt-induced cytokine production in murine airway epithelial cells from Par2-KO mice was not significantly different from the WT cells. Consistently, PAR2 knockdown in human cells also had no effect on cytokine expression. In contrast, the cytokine expressions induced by synthetic PAR2 agonist or other asthma-related allergens (e.g. cockroach extracts) were indeed mediated via a PAR2-dependent mechanism. Finally, we found that EGFR pathway was responsible for Alt-induced epithelial cytokine expression. Conclusion The activation of EGFR, but not PAR2, was likely to drive the airway inflammation and epithelial cytokine production induced by Alt.

The fungal genus Alternaria comprises a large number of asexual taxa with diverse ecological, morphological and biological modes ranging from saprophytes to plant pathogens. Understanding the speciation processes affecting asexual fungi is important for estimating biological diversity, which in turn affects plant disease management and quarantine enforcement. This study included 106 isolates of Alternaria representing five phylogenetically defined clades in two sister sub‐generic groups: section Porri (A. dauci, A. solani and A. limicola) and section Alternaria (A. alternata/tenuissima and A. arborescens). Species in section Porri are host‐specific while species in section Alternaria have wider host ranges. For each isolate, DNA sequences of three genes (Alt a1, ATPase, Calmodulin) were used to estimate phylogenies at the population and species levels. Three multilocus haplotypes were distinguished among A. dauci isolates and only one haplotype among A. solani and A. limicola isolates, revealing low or no differentiation within each taxon and strong clonal structure for taxa in this section. In contrast, 37 multilocus haplotypes were found among A. alternata/tenuissima isolates and 21 multilocus haplotypes among A. arborescens isolates, revealing much higher genotypic diversity and multiple clonal lineages within taxa, which is not typical of asexual reproducing lineages. A species tree was inferred using a Yule Speciation model and a strict molecular clock assumption. Species boundaries were well defined within section Porri. However, species boundaries within section Alternaria were only partially resolved with no well‐defined species boundaries, possibly due to incomplete lineage sorting. Significant association with host specificity seems a driving force for speciation.

This study examined the genetic diversity of small-spored Alternaria species in the southwest desert of the USA by sampling 552 isolates from different habitats (soil and plant debris) in different locations (urban and an undisturbed desert). To estimate the genetic diversity, Amplified Fragment Length Polymorphism (AFLP) fingerprinting analysis was performed for all isolates. Strains representative of the sampled genotypic diversity (n = 125) were further characterized according their sporulation pattern and the capability to produce allergens. Morphological characterization assigned the majority of the strains to the Alternaria alternata and Alternaria tenuissima morpho-groups with only two isolates assigned to the Alternaria arborescens morpho-group. AFLP fingerprinting differentiated the A. arborescens morpho-groups, but could not distinguish between the A. alternata and A. tenuissima morpho-groups. Western blot analysis showed that a large number of allergenic proteins were produced by strains. These proteins were not specific for any morpho-group nor source of isolation. A hierarchical analysis of molecular variance was performed on the AFLP data to quantify molecular variation and partition this variation among sampled locations and habitat. No statistically significant differentiation among locations and habitat was detected indicating a lack of population structure across environments.

In 2014 an unidentified disease was found on lettuce and celery grown in the Salinas Valley, Monterey Co., CA. Lettuce leaf symptoms were round to oval spots, 2 to 4 mm in diameter, white to tan, with a brown border. Celery leaf spots were round to oval, 2 to 4 mm in diameter, white to tan, with a chlorotic border. Initially it was thought that the damage was caused by chemical drift; however, field personnel noted the association of the disease with nearby carrots infected with Alternaria leaf blight. Microscopic examination of lettuce and celery leaves showed obclavate, brown, multicelled conidia in the spot centers, and a fungus was consistently isolated from this tissue. Cultural, morphological, and molecular analyses confirmed the fungus to be Alternaria dauci. Isolates of A. dauci from lettuce, celery, and carrot were pathogenic on all three crops. Field surveys showed that disease severity was greatest on the side of the lettuce or celery field closest to carrots. This is the first documentation that the carrot pathogen A. dauci can cause a disease on lettuce and celery grown in the field. The disease is designated as Alternaria leaf speck. Alternaria dauci was consistently isolated from nearby spinach plants showing identical symptoms and signs. However, pathogenicity tests were inconsistent and additional studies are needed to document A. dauci on spinach.

Aflatoxins are highly carcinogenic secondary metabolites that can contaminate approximately 25% of crops and that cause or exacerbate multiple adverse health conditions, especially in Sub-Saharan Africa and South and Southeast Asia. Regulation and decontamination of aflatoxins in high exposure areas is lacking. Biological detoxification methods are promising because they are assumed to be cheaper and more environmentally friendly compared to chemical alternatives. White-rot fungi produce non-specific enzymes that are known to degrade aflatoxin in in situ and ex situ experiments. The aims of this study were to (1) decontaminate aflatoxin B1 (AFB1) in naturally contaminated maize with the edible, white-rot fungus Pleurotus ostreatus (oyster mushroom) using a solid-state fermentation system that followed standard cultivation techniques, and to (2) and to assess the risk of mutagenicity in the resulting breakdown products and mushrooms. Vegetative growth and yield characteristics of P. ostreatus were not inhibited by the presence of AFB1. AFB1 was degraded by up to 94% by the Blue strain. No aflatoxin could be detected in P. ostreatus mushrooms produced from AFB1-contaminated maize. Moreover, the mutagenicity of breakdown products from the maize substrate, and reversion of breakdown products to the parent compound, were minimal. These results suggest that P. ostreatus significantly degrades AFB1 in naturally contaminated maize under standard cultivation techniques to levels that are acceptable for some livestock fodder, and that using P. ostreatus to bioconvert crops into mushrooms can reduce AFB1-related losses.

approach DTU Orbit (14/08/2019) Characterization of small-spored Alternaria from Argentinean crops through a polyphasic approach Small-spored Alternaria have been isolated from a wide variety of food crops, causing both economic losses and human health risk due to the metabolites produced. Their taxonomy has been discussed widely, but no scientific consensus has been established in this field to date. Argentina is a major exporter of agricultural products, so it is essential to thoroughly understand the physiological behaviour of this pathogen in a food safety context. Thus, the objective of this work was to characterize small-spored Alternaria spp. obtained from tomato fruits, pepper fruits, wheat grains and blueberries from Argentina by a polyphasic approach involving metabolomic and phylogenetic analyses based on molecular and morphological characters. Morphological analysis divided the population studied into three groups; A. arborescens sp.grp., A. tenuissima sp.-grp., and A. alternata sp.-grp. However, when these characters were simultaneously analysed with molecular data, no clearly separated groups were obtained. Haplotype network and phylogenetic analysis (both Bayesian and maximum parsimony) of a conserved region yielded the same result, suggesting that all isolates belong to the same species. Furthermore, no correlation could be established between morphological species-groups and a metabolite or group of metabolites synthesized. Thus, the whole set of analyses carried out in the present work supports the hypothesis that these small-spored Alternaria isolates from food belong to the same species. Identification at species level through classical morphology or modern molecular techniques does not seem to be a useful tool to predict toxicological risk in food matrices. The detection of any small-spored Alternaria from Section Alternaria (D.P. Lawr., Gannibal, Peever & B.M. Pryor 2013) in food implies a potential toxicological risk.

Alternaria heart rot of pomegranate fruit is generally considered a minor disease. However, the current listing of the causal pathogen in California as "Alternaria sp." or as "A. alternata and other Alternaria spp." restricts trade of the crop to some major export markets where quarantines are in place in an effort to prevent the spread of unknown or undescribed pathogens. Thus, species identification of the pathogen is critical in determining whether infected fruit should be regulated by quarantines. In this study, 86 isolates of Alternaria were collected from pomegranate fruit with Alternaria heart rot symptoms from major production areas in California. An unweighted pair group method with arithmetic means analysis based on amplified fragment length polymorphisms revealed two main clusters, each with a high degree of variability. One of the clusters contained 24 isolates from pomegranate and one reference isolate of Alternaria arborescens. Reference isolates of A. alternata and A. tenuissima were found among pomegranate isolates in the other cluster, and these two species could not be separated. In maximum-parsimony analysis of ribosomal DNA internal transcribed spacer sequence data, representative pomegranate isolates all clustered with reference sequences of species in section Alternaria. Single-nucleotide differences separated A. arborescens, A. gaisen, and two pomegranate isolates from the majority of the remaining isolates. Sequence comparisons of gapdh and OPA10-2 loci indicated that none of the pomegranate isolates were identical to A. gaisen, which is a quarantine pathogen. Due to high genetic similarity and variability of morphological characteristics, revisions of the taxonomy of small-spored Alternaria spp. have been proposed by others. Based on this recent taxonomic work and work herein by us, pomegranate isolates from California can be assigned to A. alternata and A. arborescens. Reassessment of export restrictions for California pomegranate due to the previous pathogen classification is warranted. Fruit injection inoculations with conidia of 12 representative isolates 3 months before harvest caused typical symptoms of Alternaria heart rot, whereas flower inoculations did not result in fruit disease.

Research on the distribution and structure of fungal communities in caves is lacking. Kartchner Caverns is a wet and mineralogically diverse carbonate cave located in an escarpment of Mississippian Escabrosa limestone in the Whetstone Mountains, Arizona, USA. Fungal diversity from speleothem and rock wall surfaces was examined with 454 FLX Titanium sequencing technology using the Internal Transcribed Spacer 1 as a fungal barcode marker. Fungal diversity was estimated and compared between speleothem and rock wall surfaces, and its variation with distance from the natural entrance of the cave was quantified. Effects of environmental factors and nutrient concentrations in speleothem drip water at different sample sites on fungal diversity were also examined. Sequencing revealed 2,219 fungal operational taxonomic units (OTUs) at the 95 % similarity level. Speleothems supported a higher fungal richness and diversity than rock walls. However, community membership and the taxonomic distribution of fungal OTUs at the class level did not differ significantly between speleothems and rock walls. Both OTU richness and diversity decreased significantly with increasing distance from the natural cave entrance. Community membership and taxonomic distribution of fungal OTUs also differed significantly between the sampling sites closest to the entrance and those furthest away. There was no significant effect of temperature, CO 2 concentration, or drip water nutrient concentration on fungal community structure on either speleothems or rock walls. Together, these results suggest that proximity to the natural entrance is a critical factor in determining fungal community structure on mineral surfaces in Kartchner Caverns.

Background Alternaria is considered one of the most common saprophytic fungal genera on the planet. It is comprised of many species that exhibit a necrotrophic phytopathogenic lifestyle. Several species are clinically associated with allergic respiratory disorders although rarely found to cause invasive infections in humans. Finally, Alternaria spp. are among the most well known producers of diverse fungal secondary metabolites, especially toxins. Description We have recently sequenced and annotated the genomes of 25 Alternaria spp. including but not limited to many necrotrophic plant pathogens such as A. brassicicola (a pathogen of Brassicaceous crops like cabbage and canola) and A. solani (a major pathogen of Solanaceous plants like potato and tomato), and several saprophytes that cause allergy in human such as A. alternata isolates. These genomes were annotated and compared. Multiple genetic differences were found in the context of plant and human pathogenicity, notably the pro-inflammatory potential of A. alternata . The Alternaria genomes database was built to provide a public platform to access the whole genome sequences, genome annotations, and comparative genomics data of these species. Genome annotation and comparison were performed using a pipeline that integrated multiple computational and comparative genomics tools. Alternaria genome sequences together with their annotation and comparison data were ported to Ensembl database schemas using a self-developed tool (EnsImport). Collectively, data are currently hosted using a customized installation of the Ensembl genome browser platform. Conclusion Recent efforts in fungal genome sequencing have facilitated the studies of the molecular basis of fungal pathogenicity as a whole system. The Alternaria genomes database provides a comprehensive resource of genomics and comparative data of an important saprophytic and plant/human pathogenic fungal genus . The database will be updated regularly with new genomes when they become available. The Alternaria genomes database is freely available for non-profit use at http://alternaria.vbi.vt.edu .

The infectoria species-group within the genus Alternaria was originally conceived by Simmons in 1993 and was based upon common morphological characteristics that included the development of conidial chains with primary, secondary, and tertiary branching resulting in substantial three-dimensional complexity. These characters can overlap to varying degrees with numerous taxa in another Alternaria group, the alternata species-group, making species-group differentiation difficult. However, members of the infectoria species-group are also distinguished from other small-spored Alternaria species based upon colony characteristics that typically include white or nearly white floccose colonies on DRYES medium and clumps of sporulation islands on low sugar media such as V8 agar, PCA, and weak PDA. In addition, the infectoria species-group contains representatives that are known to produce teleomorphs (Lewia), whereas the members of the alternata species-group and other Alternaria species-groups are strictly asexual. In this study, an assemblage of isolates recovered from varied hosts from the west coast of the United States were examined based upon morphological characters and compared to previously described members of the infectoria species-group. These isolates and members of the infectoria species-group typically produce arachnoid vegetative hyphae with multiple primary conidiophores, whereas other small-spored Alternaria species produce primary conidiophores predominately directly from the agar surface. Additionally, molecular phylogenetic analyses resolved these isolates and members of the infectoria species-group as distinctly nested amongst other sexual taxa in Allewia (Embellisia anamorph) and Macrospora (Nimbya anamorph) and phylogenetically distant to asexual lineages of Alternaria. One taxon among these isolates was novel and clustered with the asexual A. rosae in a distinct clade basal to all other members of the infectoria species-group. A new genus is proposed, Pseudoalternaria gen. nov. and a new taxon is described, Pseudoalternaria arrhenatheria sp. nov.. Moreover, a second taxon is reclassified, Pseudoalternaria rosae comb. nov.

BACKGROUND:Traditional morphological and biological species concepts are difficult to apply to closely related, asexual taxa because of the lack of an active sexual phase and paucity of morphological characters. Phylogenetic species concepts such as genealogical concordance phylogenetic species recognition (GCPSR) have been extensively used; however, methods that incorporate gene tree uncertainty into species recognition may more accurately and objectively delineate species. Using a worldwide sample of Alternaria alternata sensu lato, causal agent of citrus brown spot, the evolutionary histories of four nuclear loci including an endo-polygalacturonase gene, two anonymous loci, and one microsatellite flanking region were estimated using the coalescent. Species boundaries were estimated using several approaches including those that incorporate uncertainty in gene genealogies when lineage sorting and non-reciprocal monophyly of gene trees is common.RESULTS:Coalescent analyses revealed three phylogenetic lineages strongly influenced by incomplete lineage sorting and recombination. Divergence of the citrus 2 lineage from the citrus 1 and citrus 3 lineages was supported at most loci. A consensus of species tree estimation methods supported two species of Alternaria causing citrus brown spot worldwide. Based on substitution rates at the endo-polygalacturonase locus, divergence of the citrus 2 and the 1 and 3 lineages was estimated to have occurred at least 5, 400 years before present, predating the human-mediated movement of citrus and associated pathogens out of SE Asia.CONCLUSIONS:The number of Alternaria species identified as causing brown spot of citrus worldwide using morphological criteria has been overestimated. Little support was found for most of these morphospecies using quantitative species recognition approaches. Correct species delimitation of plant-pathogenic fungi is critical for understanding the evolution of pathogenicity, introductions of pathogens to new areas, and for regulating the movement of pathogens to enforce quarantines. This research shows that multilocus phylogenetic methods that allow for recombination and incomplete lineage sorting can be useful for the quantitative delimitation of asexual species that are morphologically indistinguishable. Two phylogenetic species of Alternaria were identified as causing citrus brown spot worldwide. Further research is needed to determine how these species were introduced worldwide, how they differ phenotypically and how these species are maintained.

A recent study on fungal mating type genes revealed two MAT alleles within homothallic Sclerotinia sclerotiorum differentiated by an inversion, Inv− (inversion negative) and Inv+ (inversion positive). An analysis of mating type in closely related S. minor was conducted to shed light on the evolution of this MAT inversion. Inv− and Inv+ MAT alleles were identified in S. minor and were characterized. Both MAT alleles in S. minor were flanked by APN2 and SLA2, and consisted of two idiomorphs fused as in other homothallic ascomycetes. However, in the Inv+ MAT, the 3·6 kb MAT region was inverted relative to the Inv− MAT. Except for the inversion, both Inv− and Inv+ MAT in S. minor were equal in size and identical in nucleotide sequence. The MAT inversion in Inv+ S. minor was at exactly the same place as in Inv+ S. sclerotiorum and affected three of four MAT genes: MAT1‐1‐1 was truncated and MAT1‐2‐4 and MAT1‐2‐1 were inverted. Unlike S. sclerotiorum, expression of MAT genes did not differ between Inv− and Inv+ S. minor. The 250 bp inverted repeat motif that flanked the inverted MAT region in S. sclerotiorum and believed responsible for the MAT inversion was also found in S. minor, but was 256 bp. Depending on the MAT genes, 93–96% nucleotide identity was observed between Sclerotinia species. Both Inv+ and Inv− MAT S. minor and S. sclerotiorum isolates were commonly found in lettuce fields of Arizona along with MAT heterokaryons.

The systematics of Alternaria and allied genera traditionally has been based on the characteristics of conidia and the sporulation apparatus. This emphasis on morphology in the reconstruction of organismal relationships has resulted in taxonomic uncertainty and flux for a number of taxa in Alternaria and the related genera Stemphylium, Embellisia, Nimbya and Ulocladium. The present study used a molecular phylogenetic approach for systematic resolution and incorporated extensive taxon sampling (n = 176 species) representing 10 genera and analyses of 10 protein-coding loci. Phylogenetic analyses based on five of these genes revealed eight distinct asexual lineages of Alternaria that cluster as the sister group to the asexual paraphyletic genus Ulocladium, while taxa with known teleomorphs currently circumscribed as Alternaria (the infectoria species-group) cluster among genera that also have representatives with known teleomorphs. This work proposes to elevate the eight well supported asexual lineages of Alternaria to the taxonomic rank of section. Evolutionary relationships among Alternaria and closely related genera are discussed.

Isothiocyanates (ITCs) is a group of defense related compounds synthesized byBrassicas that have positive effects on human health which suggest that they are environmentally friendly compounds to control fungi infections. However, the development of ITC-resistant strains of fungi is a matter of concern. The objective of the present work was to study the response of Alternaria alternata to allyl-isothiocyanate (AITC) and benzyl isothiocyanate (BITC) chronic exposure and the effect of the treatment on some of the inter simple sequence repeats (ISSR) regions. Five strains of A. alternata isolated from tomato and five isolated from cabbage were independently exposed in vitro to AITC and BITC. Concentrations were increased until it reached 0.08 and 0.6 mg/mL of AITC and BITC, respectively. Genomic DNA from both wild type and isogenic adapted strains to ITCs was isolated and five primers were used for ISSR amplification: (GACA)4: 5´-GACAGACAGACAGACA-3´; M13:5´-GAGGGTGGCGGCGGTTCT-3´;(AAG)8:5´-AAGAAGAAGAAGAAGAAGAAGAAG-3´; (ACA)5: 5´-ACAACAACAACAACA-3´ and T3B: 5´-AGGTCGCGGGTTCGAATCC-3´. A lower degree of polymorphism was found to be induced by the treatment in the wild-type strains isolated from cabbage as compared with the wild-type strains isolated from tomato. It can be concluded that ITCs exposure induced random mutations in different ISSR regions of the A. alternata genome which does not lead to the development of strains with a hereditable resistant phenotype. Key words: Alternaria alternata, fungicide, allyl-isothiocyanate, benzyl-isothiocyanate, inter-simple sequence repeat

Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO2-fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin–Benson–Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO2-fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.