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At least 487 records · Page 27

The Study of Microbial Physiology Under Microoxic Conditions Is Critical but Neglected

ABSTRACT During the early evolution of life on Earth, the environment was largely free of molecular oxygen, and only anaerobic life existed. With the subsequent oxidation of oceans and the atmosphere, a wide range of environmental niches, ranging from anoxic to microoxic/hypoxic and oxic, developed. Despite this broad range of natural environments, microbiology as a field has focused on the physiology, metabolism, and genetics of aerobic microorganisms, with less attention paid to anaerobes and much less attention paid to microaerophiles. The disparity in studies between aerobic and anaerobic conditions is rampant in host‐associated systems, particularly in human health, and studies of microorganisms in intermediate oxygen conditions between fully aerobic and fully anoxic conditions are exceedingly rare. Studies on the physiological behaviour, metabolism, growth response, and drug susceptibility patterns of commensal and pathogenic organisms are almost totally neglected in microoxic conditions. Furthermore, microorganisms from microaerobic and microoxic ecosystems have been less robustly explored in terms of physiology, growth, and metabolism. In this work, we highlight the importance of understanding the physiological and metabolic behaviours of microorganisms under hypoxic or microoxic conditions.

Environmental Sciences & Ecology↗

Balancing Trade-Offs Imposed by Growth Media and Mass Spectrometry for Bacterial Exometabolomics

The bacterial exometabolome consists of a vast array of specialized metabolites, many of which are only produced in response to specific environmental stimuli. For this reason, it is desirable to control the extracellular environment with a defined growth medium composed of pure ingredients. However, complex (undefined) media are expected to support the robust growth of a greater variety of microorganisms than defined media. Here, we investigate the trade-offs inherent to a range of complex and defined solid media for the growth of soil microorganisms, production of specialized metabolites, and detection of these compounds using direct infusion mass spectrometry. We find that complex media support growth of more soil microorganisms, as well as allowing for the detection of more previously discovered natural products as a fraction of total m/z features detected in each sample. However, the use of complex media often caused mass spectrometer injection failures and poor-quality mass spectra, which in some cases resulted in over a quarter of samples being removed from analysis. Defined media, while more limiting in growth, generated higher quality spectra and yielded more m/z features after background subtraction. These results inform future exometabolomic experiments requiring a medium that supports the robust growth of many soil microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗

Carbon Amendments Alter Microbial Community Structure and Net Mercury Methylation Potential in Sediments

ABSTRACT Neurotoxic methylmercury (MeHg) is produced by anaerobic Bacteria and Archaea possessing the genes hgcAB , but it is unknown how organic substrate and electron acceptor availability impacts the distribution and abundance of these organisms. We evaluated the impact of organic substrate amendments on mercury (Hg) methylation rates, microbial community structure, and the distribution of hgcAB + microbes with sediments. Sediment slurries were amended with short-chain fatty acids, alcohols, or a polysaccharide. Minimal increases in MeHg were observed following lactate, ethanol, and methanol amendments, while a significant decrease (∼70%) was observed with cellobiose incubations. Postincubation, microbial diversity was assessed via 16S rRNA amplicon sequencing. The presence of hgcAB + organisms was assessed with a broad-range degenerate PCR primer set for both genes, while the presence of microbes in each of the three dominant clades of methylators ( Deltaproteobacteria , Firmicutes , and methanogenic Archaea ) was measured with clade-specific degenerate hgcA quantitative PCR (qPCR) primer sets. The predominant microorganisms in unamended sediments consisted of Proteobacteria , Firmicutes , Bacteroidetes , and Actinobacteria . Clade-specific qPCR identified hgcA + Deltaproteobacteria and Archaea in all sites but failed to detect hgcA + Firmicutes . Cellobiose shifted the communities in all samples to ∼90% non- hgcAB -containing Firmicutes (mainly Bacillus spp. and Clostridium spp.). These results suggest that either expression of hgcAB is downregulated or, more likely given the lack of 16S rRNA gene presence after cellobiose incubation, Hg-methylating organisms are largely outcompeted by cellobiose degraders or degradation products of cellobiose. These results represent a step toward understanding and exploring simple methodologies for controlling MeHg production in the environment. IMPORTANCE Methylmercury (MeHg) is a neurotoxin produced by microorganisms that bioacummulates in the food web and poses a serious health risk to humans. Currently, the impact that organic substrate or electron acceptor availability has on the mercury (Hg)-methylating microorganisms is unclear. To study this, we set up microcosm experiments exposed to different organic substrates and electron acceptors and assayed for Hg methylation rates, for microbial community structure, and for distribution of Hg methylators. The sediment and groundwater was collected from East Fork Poplar Creek in Oak Ridge, TN. Amendment with cellobiose (a lignocellulosic degradation by-product) led to a drastic decrease in the Hg methylation rate compared to that in an unamended control, with an associated shift in the microbial community to mostly nonmethylating Firmicutes . This, along with previous Hg-methylating microorganism identification methods, will be important for identifying strategies to control MeHg production and inform future remediation strategies.

16S↗

Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep

We report Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b (“Candidatus Methanocomedenaceae”) and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.

59 BASIC BIOLOGICAL SCIENCES↗

Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis [plus supplementary information]

Pretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a complex microbial community at the level of gene transcription and doing so with genome resolution. Specific organisms were discovered that could simultaneously tolerate a moderate IL concentration and transcribe a diverse array of cellulolytic enzymes. Gene sequences of cellulolytic enzymes and efflux pumps from those same organisms were also identified, providing important resources for future research on engineering IL-tolerant organisms and enzymes. Ionic liquid (IL) pretreatment is a promising approach for the conversion of lignocellulose to biofuels. The toxicity of residual IL, however, negatively impacts the performance of industrial enzymes and microorganisms in hydrolysis and fermentation. In this study, a thermophilic microbial community was cultured on switchgrass amended with various levels of the ionic liquid 1-ethyl-3-methylimidazolium acetate. Changes in the microbial community composition and transcription of genes relevant to IL tolerance and lignocellulose hydrolysis were quantified. Increasing the level of IL to 0.1% (wt) led to increased levels of relative abundance and transcription in organisms of the phylum Firmicutes . Interestingly, IL concentrations of up to 1% (wt) also resulted in greater xylanase transcription and enzyme activity as well as increased transcription of endoglucanase, beta-glucosidase, and IL tolerance genes compared to communities without IL. IL levels above 1% (wt) resulted in decreased enzyme activity and transcription of genes involved in lignocellulose hydrolysis. The results indicate that moderate levels of IL select for thermophilic microorganisms that not only tolerate IL but also effectively hydrolyze lignocellulose from switchgrass. Discovery of IL-tolerant organisms and enzymes is critical for the development of biological processes that convert IL-pretreated biomass to biofuels and chemicals. Employing metatranscriptomic analysis of enrichment cultures can facilitate the discovery of microorganisms and enzymes that may be active in the presence of toxic compounds such as ionic liquids.

09 BIOMASS FUELS↗

RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids

Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve the understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were larger than other described plasmids, which is a trait associated with plasmid mobility. There was a weak relationship between chromosome size and plasmid size and no relationship between chromosome size and plasmid number, suggesting that these genomic traits are independent in soil. We used RefSoil+ to inform the distributions of antibiotic resistance genes among soil microorganisms compared to those among nonsoil microorganisms. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a reference for the diversity, composition, and host associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves the understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances.Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource of important plasmid-associated genes, including antibiotic resistance genes.

59 BASIC BIOLOGICAL SCIENCES↗

ShadeLab/RefSoil_plasmids

Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve the understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were larger than other described plasmids, which is a trait associated with plasmid mobility. There was a weak relationship between chromosome size and plasmid size and no relationship between chromosome size and plasmid number, suggesting that these genomic traits are independent in soil. We used RefSoil+ to inform the distributions of antibiotic resistance genes among soil microorganisms compared to those among nonsoil microorganisms. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a reference for the diversity, composition, and host associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves the understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances.

Dunivin, Taylor↗

Association Between Preoperative Muscle Mass and Intraoperative Bacterial Translocation in Patients Undergoing Hepatectomy, Pancreatoduodenectomy, and Esophagectomy

Purpose: This study investigated the correlation between the fecal profile and muscle mass, which has not been elucidated before. Methods: This study included patients who underwent hepatectomy, pancreatoduodenectomy, or esophagectomy and had fecal samples collected preoperatively and mesenteric lymph nodes (MLNs) harvested intraoperatively to determine the fecal profile and presence of bacteria in the MLNs. Total psoas area (TPA) was measured at the third lumbar vertebra using preoperative computed tomography images. TPA was standardized by body surface area (BSA) using the following equation: standardized TPA (mm{sup 2}/m{sup 2}) (stTPA) = TPA (mm{sup 2})/BSA (m{sup 2}). The fecal concentrations of representative microorganisms and organic acids also were measured. Results: A total of 127 patients undergoing hepatectomy (n = 48), pancreatoduodenectomy (n = 44), and esophagectomy (n = 35) were included. The fecal levels of predominant obligate anaerobes showed a positive correlation with stTPA, whereas that of pathogenic microorganisms showed a negative correlation with stTPA. The fecal concentrations of total short chain fatty acids (the sum of acetic acid, propionic acid, and butyric acid) also showed a positive correlation with stTPA. The stTPA was significantly lower in patients with positive microorganisms in the MLNs (patients with bacterial translocation) compared to those without microorganisms in the MLNs (p = 0.047). Conclusions: This study was the first to demonstrate the association between muscle mass and the fecal profile, as well as their association with bacterial translocation.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Comparative analysis of uranium bioassociation with halophilic bacteria and archaea

Rock salt represents a potential host rock formation for the final disposal of radioactive waste. The interactions between indigenous microorganisms and radionuclides, e.g. uranium, need to be investigated to better predict the influence of microorganisms on the safety assessment of the repository. Hence, the association process of uranium with two microorganisms isolated from rock salt was comparatively studied. Brachybacterium sp. G1, which was isolated from the German salt dome Gorleben, and Halobacterium noricense DSM15987T , were selected as examples of a moderately halophilic bacterium and an extremely halophilic archaeon, respectively. The microorganisms exhibited completely different association behaviors with uranium. While a pure biosorption process took place with Brachybacterium sp. G1 cells, a multistage association process occurred with the archaeon. In addition to batch experiments, in situ attenuated total reflection Fourier-transform infrared spectroscopy was applied to characterize the U(VI) interaction process. Biosorption was identified as the dominating process for Brachybacterium sp. G1 with this method. Carboxylic functionalities are the dominant interacting groups for the bacterium, whereas phosphoryl groups are also involved in U(VI) association by the archaeon H. noricense.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metabolic Engineering and Modeling of Metabolic Pathways to Improve Hydrogen Production by Photosynthetic Bacteria

Rising energy demands and the imperative to reduce carbon dioxide (CO 2 ) emissions are driving research on biofuels development. Hydrogen gas (H 2 ) is one of the most promising biofuels and is seen as a future energy carrier by virtue of the fact that 1) it is renewable, 2) does not evolve the “greenhouse gas” CO 2 in combustion, 3) liberates large amounts of energy per unit weight in combustion (having about 3 times the energy content of gasoline), and 4) is easily converted to electricity by fuel cells. Among the various bioenergy strategies, environmental groups and others say that the concept of the direct manufacture of alternative fuels, such as H 2 , by photosynthetic organisms is the only biofuel alternative without significant negative criticism [1]. Biological H 2 production by photosynthetic microorganisms requires the use of a simple solar reactor such as a transparent closed box, with low energy requirements, and is considered as an attractive system to develop as a biocatalyst for H 2 production [2]. Various purple bacteria including Rhodopseudomonas palustris, can utilize organic substrates as electron donors to produce H 2 at the expense of solar energy. Because of the elimination of energy cost used for H 2 O oxidation and the prevention of the production of O 2 that inhibits the H 2 -producing enzymes, the efficiency of light energy conversion to H 2 by anoxygenic photosynthetic bacteria is in principle much higher than that by green algae or cyanobacteria, and is regarded as one of the most promising cultures for biological H 2 production [3]. Here implemented a simple and relatively straightforward strategy for hydrogen production by photosynthetic microorganisms using sunlight, sulfur- or iron-based inorganic substrates, and CO 2 as the feedstock. Carefully selected microorganisms with bioengineered beneficial traits act as the biocatalysts of the process designed to both enhance the system efficiency of CO 2 fixation and the net hydrogen production rate. Additionally we applied metabolic engineering approaches guided by computational modeling for the chosen model microorganisms to enable efficient hydrogen production.

59 BASIC BIOLOGICAL SCIENCES↗

Integrative molecular and microanalytical studies of syntrophic partnerships linking C, S, and N cycles in anoxic environments

Syntrophy and other forms of symbiotic associations between microorganisms are central to carbon and nutrient cycling in the environment. However, the inherent interdependence of these interactions, dynamic behavior, and frequent existence at thermodynamic limits has hindered our ability to both recognize syntrophic partnerships in nature and effectively study their behavior in the laboratory. To characterize and understand the underlying factors influencing syntrophic associations within complex communities requires a suite of tools that extend beyond basic molecular identification and cultivation. This specifically includes methods that preserve the natural spatial relationships between metabolically interdependent microorganisms while allowing downstream geochemical and/or molecular analysis. With support from this award, we have developed and applied new combinations of molecular, microscopy, and stable isotope-based methodologies that enable the characterization of fundamental links between phylogenetically-identified microorganisms and their specific metabolic activities and interactions in the environment. Through the coupling of fluorescence in situ hybridization (FISH) with cell capture and targeted metagenomics (Magneto-FISH), and FISH + secondary ion mass spectrometry (i.e. FISH-SIMS or FISH-nanoSIMS), we have defined new microbial interactions and the ecophysiology of anaerobic microorganisms involved in environmental methane cycling.

03 NATURAL GAS↗

Ocular Pathogens, Eye Infections, and Cosmetics Periodic Update (July 1, 2016 to June 30, 2017)

A PubMed literature search was conducted to support analyses and investigations of the relationship between microorganisms associated with human eye infections (including opportunistic pathogens) and cosmetics. Key terms for PubMed literature searches included; microbial genera and species of interest (bacteria, viruses, fungi, protozoans, parasites), opportunistic pathogens, human eye disease and infection, human ocular infections, specific eye diseases (keratitis, conjunctivitis, etc.), eye accidents, eye surgery, contacts, infants, pregnant women, geriatric, immunocompromised, HIV and polymicrobial. The number of journal articles for defined searches was summarized and journal citations and abstracts were cataloged and incorporated into a searchable information system (MS Access). A periodic update to the literature searches was conducted in July 2017 and observations from the update indicate the most commonly associated bacteria with eye infections/diseases were Staphylococcus sp., Chlamydia sp. and Pseudomonas sp. Also, the literature searches indicate the most commonly associated fungi with eye infections/diseases were Fusarium sp., Aspergillus sp. and Candida sp. A relative rank of occurrence of microorganisms associated with eye infections/disease in the literature citations was; Staphylococcus aureus, Chlamydia trachomatis, Cytomegalovirus, Herpes zoster virus, Pseudomonas aeruginosa, Staphylococcus epidermidis, Acanthamoeba sp., Fusarium sp., E. coli and Mycobacterium tuberculosis. Literature searches for opportunistic microorganisms and emerging pathogens for this update identified several articles on fungi, Bacillus sp. (primarily B. cereus), Haemophilus influenzae and Human Papillomavirus (HPV) associated with eye infections/diseases. Although the literature searches focused on microorganisms, key eye diseases noted in the citations were keratitis, conjunctivitis, corneal ulcers, endophthalmitis and keratoconjunctivitis.

60 APPLIED LIFE SCIENCES↗

Topical Pathogens, Topical (Skin) Infections, and Cosmetics Periodic Update (July 1, 2016 to June 30, 2017)

A literature search was conducted of PubMed/Medline and MESH databases to support analyses and investigations of the relationship between microorganisms associated with human topical (skin) infections (including opportunistic pathogens) and cosmetics. Key terms for literature searches included; microbial genera and species of interest (bacteria, viruses, fungi, protozoans, parasites), opportunistic pathogens, human skin disease and infection, specific skin diseases (e.g., dermatomycoses, candidiasis, ecthyma, impetigo, etc.), surgery, infants, pregnant women, geriatric, immunocompromised, HIV and polymicrobial. The number of journal articles for defined searches was summarized and journal citations and abstracts were cataloged and incorporated into a searchable information system (MS Access). A periodic update to literature searches was completed in July 2017 and observations from the update indicate the most commonly associated bacteria with topical (skin) infections/diseases were Staphylococcus spp., Streptococcus spp., and Pseudomonas spp. Also, the literature searches indicate the most commonly associated fungi with topical (skin) infections/diseases were Tinea spp., Candida spp., and Aspergillus spp. A relative rank of occurrence of microorganisms associated with topical (skin) infections/disease in the literature citations was: Herpes simplex virus, Staphylococcus aureus, Tinea spp., Candida spp., Human papillomavirus, Pseudomonas aeruginosa, Leishmania spp., Streptococcus spp., Aspergillus spp., and Treponema pallidum. Literature searches for opportunistic microorganisms and emerging pathogens for this update identified several articles on dermatomycotic species including Candida yeasts (Candida albicans), dermatophytes (Aspergillus, and Trichophyton) and other opportunistic yeasts (Malassezia spp. and Rhodotorula spp.) associated with topical (skin) infections/diseases. A few of the opportunistic pathogenic Enterobacteriaceae more prevalent in citations were Klebsiella spp. and Enterobacter spp. Although the literature searches focused on microorganisms, key topical (skin) diseases noted in the citations were dermatomycoses, leishmaniasis, eczema, candidiasis, and impetigo.

60 APPLIED LIFE SCIENCES↗

Multi-‘omic’ analyses of the dynamics, mechanisms, and pathways for carbon turnover in grassland soil under two climate regimes

Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. This knowledge gap precludes meaningful predictions of relationships between microorganism types and their biogeochemical functions. Specifically, as climate change physically alters terrestrial ecosystems, the impact on microbial consortia and potential consequences for release of carbon and other nutrients from soils are difficult to predict. In this project, we investigated the identities, activity, and functional potential of microorganisms residing in a well characterized grassland ecosystem (the Angelo Coast Range Reserve) undergoing a controlled 14-year rainfall extension climate change experiment. The research was achieved using a combination of “omics”-based technologies, including genome-resolved metagenomics, transcriptomics, and proteomics. The approach allowed us to capture multiple facets of community ecology and activity in situ. Supported by this award, significant progress was made in addressing the grand challenge of achieving genome-resolution for very complex soil microbial communities. In addition to improvements in the methodology, the research required new approaches to define the 3-dimentional distributions of microorganisms and their metabolic traits in soils and to decipher the impact of climate. Underpinning such analyses was the need for sufficient statistical power to test for geographic, soil depth and rainfall controls on community composition and metabolic properties. This required that we scale up throughput substantially. We overcame significant technical barriers to achieve complex microbial community resolution.

54 ENVIRONMENTAL SCIENCES↗

Life on the Edge: Microbes in Rock Varnish

The newly discovered high concentrations of manganese on Mars open up new possibilities for habitability on that planet [1, 2]. On Earth, there is a close association between Mn deposits and the presence of Mn- and Fe- oxidizing microbes [3-7]; as such, Mn is considered a principal biosignature for Mars [8]. The most common terrestrial Mn-rich surface material on Earth is desert varnish, a dark, shiny coating on rocks in arid locations. Microorganisms occupy various niches within rock varnish, and it is probable that the concentration of Mn in many rock varnishes is mediated by microbial activity [6, 9, 10]; however, the relationship between microbes and varnish remains a source of long-standing controversy [11]. Do microorganisms drive the formation of varnish, oxidizing Mn and Fe to gain energy, or do they instead utilize varnish as a habitat? This long-standing question has important implications for our understanding of how life on Earth has evolved to capture and harness energy from the physical environment. Additionally, it will greatly influence the search on Mars for the signatures of life that may be present in rock varnish cannot be definitively identified on Mars without first being identified on Earth. Here we explored the microbial species and processes involved in the habitation of rock varnish and identified organic biosignatures that, in concert with trace element and mineralogy, could be used to distinguish the biogenic and abiogenic origins of terrestrial Mn-rich surfaces so that we may then apply the knowledge gained in this work to current Martian datasets from ChemCam. Each of these goals has important implications for our understanding of how life on Earth has evolved to capture and harness energy from the physical environment. A combinatorial experimental approach, utilizing microscopy, high-throughput DNA sequencing, culturing and physiological assays, were used to characterize the microbial communities inhabiting varnished rocks across the Western U.S. Microbial communities inhabiting varnish were shaped by both location (larger contribution) and rock type. However, we found that the unique varnish environment selects for a core group of radiation- and desiccation-tolerant microorganisms across landscapes and rock types. The bacteria comprising this core group include a who’s who of radiation resistant organisms including Rubrobacter spp., Deinococcus spp., Hymenobaceter spp., and Chroococcidiopsis spp. Among the fungi, potential lichen-forming members of the Lecanoromycetes and rock-inhabiting Dothideomycetes were common. Importantly, we found that two of the survival mechanisms employed by these microorganisms are likely key drivers of Mn oxide formation and the biogenesis of varnish. First, we showed that the key cyanobacteria inhabiting the varnish accumulate copious amounts of low molecular weight Mn2+-conjugates, that are critical for their ability to withstand the toxic effects of reactive oxygen species generated upon radiation exposure. Secondly, the microbial community inhabiting varnished rocks were found to be particularly adept at producing siderophores, which are high-affinity chelating compounds secreted by bacteria and fungi that serve to sequester Fe2+ (and Mn2+) from oxidizing environments for transport into cells as essential micronutrients for growth and survival. When tightly bound to organic ligands, Mn2+ is susceptible to oxidation to Mn3+-ligand under atmospheric oxygen and at slightly basic pH levels. Further, Mn3+-ligand can be oxidized to MnO2 (manganese oxide) when it comes into contact with reactive oxygen species (e.g., superoxide radical) formed during the photolysis of water during periods of high UV exposure. The data points towards a scenario whereby cyanobacterial biofilms, and associated radiation resistant, heterotrophic bacteria, comprise the central hub of the varnish community. These communities depend on light and water to slowly establish on the rock surface where they accumulate and concentrate Mn for survival. When the biofilms dry out, mineral rinds rich in Mn oxides form which serve as a habitat for the successive rounds of microbial growth and Mn oxide formation. Copious production and excretion of siderophores, which are extremely stable in the environment, coats the rock surface with a longlived catalyst for Mn oxidation. By discovering these two completely novel mechanisms for biogenic varnish formation, we have gained the underlying knowledge necessary to develop a suite of organic and inorganic biosignatures to distinguish biogenic and abiogenic origins of Mnrich surfaces on Earth or Mars.

59 BASIC BIOLOGICAL SCIENCES↗

Biomining Critical Elements and Metals

The US government has identified 17 critical elements, including most rare earth elements (REEs), and metals, which are used extensively in consumer electronics as well as military and national security hardware. We are developing techniques for biomining these elements, the process of using microorganisms to extract critical elements from water, ores, and mine waste to fill these needs. Bioextraction is focusing on: 1) building on our first-year successes of identifying microbes that generate exudates that enhance the extraction of multivalent cations, 2) evaluating available phosphate solubilizing microbes to dissolve apatite and monazite, and 3) and biosurfactant producing microbes. Bioaccumulation efforts involves testing microbes that: 1) naturally release complex exudates that contain organic chelating agents, and 2) naturally accumulate or hyperaccumulate (wt-% levels) metals. Results from year one includes proof of concept that biosurfactant producing microorganisms can release REEs from select ores and that release of REEs is increased by the addition of glucose. Molecular results for microorganism profiling proved a population shift after addition of microorganisms. The study will culminate in a proof-of-concept demonstration, manuscripts, and the data needed for scaledup biomining of REEs.

36 MATERIALS SCIENCE↗

How to sustainably feed a microbe: Strategies for biological production of carbon-based commodities with renewable electricity

As interest and application of renewable energy grows, strategies are needed to align the asynchronous supply and demand. Microbial metabolisms are a potentially sustainable mechanism for transforming renewable electrical energy into biocommodities that are easily stored and transported. Acetogens and methanogens can reduce carbon dioxide to organic products including methane, acetic acid, and ethanol. The library of biocommodities is expanded when engineered metabolisms of acetogens are included. Typically, electrochemical systems are employed to integrate renewable energy sources with biological systems for production of carbon-based commodities. Within these systems, there are three prevailing mechanisms for delivering electrons to microorganisms for the conversion of carbon dioxide to reduce organic compounds: (1) electrons can be delivered to microorganisms via H 2 produced separately in a electrolyzer, (2) H 2 produced at a cathode can convey electrons to microorganisms supported on the cathode surface, and (3) a cathode can directly feed electrons to microorganisms. Each of these strategies has advantages and disadvantages that must be considered in designing full-scale processes. Furthermore, this review considers the evolving understanding of each of these approaches and the state of design for advancing these strategies toward viability.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Microbial Metabolism and Community Dynamics in Hydraulic Fracturing Fluids Recovered From Deep Hydrocarbon-Rich Shale

Hydraulic fracturing is a prominent method of natural gas production that uses injected, high-pressure fluids to fracture low permeability, hydrocarbon rich strata such as shale. Upon completion of a well, the fluid returns to the surface (produced water) and contains natural gas, subsurface constituents, and microorganisms (Barbot et al., 2013; Daly et al., 2016). While the microbial community of the produced fluids has been studied in multiple gas wells, the activity of these microorganisms and their relation to biogeochemical activity is not well understood. In this experiment, we supplemented produced fluid with 13 C-labeled carbon sources (glucose, acetate, bicarbonate, methanol, or methane), and 15 N-labeled ammonium chloride in order to isotopically trace microbial activity over multiple day in anoxic incubations. Nanoscale secondary ion mass spectrometry (NanoSIMS) was used to generate isotopic images of 13 C and 15 N incorporation in individual cells, while isotope ratio monitoring–gas chromatography–mass spectrometry (IRM–GC–MS) was used to measure 13 CO 2 , and 13 CH 4 as metabolic byproducts. Glucose, acetate, and methanol were all assimilated by microorganisms under anoxic conditions. 13 CO 2 production was only observed with glucose as a substrate indicating that catabolic activity was limited to this condition. The microbial communities observed at 0, 19, and 32 days of incubation did not vary between different carbon sources, were low in diversity, and composed primarily of the class Clostridia . The primary genera detected in the incubations, Halanaerobium and Fusibacter , are known to be adapted to harsh physical and chemical conditions consistent with those that occur in the hydrofracturing environment. This study provides evidence that microorganisms in produced fluid are revivable in laboratory incubations and retained the ability to metabolize added carbon and nitrogen substrates.

59 BASIC BIOLOGICAL SCIENCES↗