A biofilm anode acclimated with acetate, acetate+methane, and methane growth media for over three years produced a steady current density of 1.6-2.3 mA/m^2 in a microbial electrochemical cell (MxC) fed with methane as the sole electron donor. Geobacter was the dominant genus for the bacterial domain (93%) in the biofilm anode, while methanogens (Methanocorpusculum labreanum and Methanosaeta concilii) accounted for 82% of the total archaeal clones in the biofilm. A fluorescence in situ hybridization (FISH) image clearly showed a biofilm of bacteria and archaea, supporting a syntrophic interaction between them for performing anaerobic oxidation of methane (AOM) in the biofilm anode. Measured cumulative coulombs correlated linearly to the methane-gas concentration in the range of 10% to 99.97% (R^2 ≥ 0.99) when the measurement was sustained for at least 50 min. Thus, cumulative coulombs over 50 min. could be used to quantify the methane concentration in gas samples. This dataset is associated with the following publication: Gao, Y., H. Ryu, B. Rittmann, A. Hussain, and H. Lee. Quantification of the methane concentration using anaerobic oxidation of methane coupled to extracellular electron transfer. Bioresource Technology. Elsevier Online, New York, NY, USA, 241: 979-984, (2017).

This study systematically assessed intracellular electron transfer (IET) and extracellular electron transfer (EET) kinetics with respect to anode potential (Eanode) in a mixed-culture biofilm anode enriched with Geobacter spp. High biofilm conductivity (0.96–1.24 mScm^-1) was maintained during Eanode changes from -0.2 to +0.2 V versus the standard hydrogen electrode (SHE), although the steady-state current density significantly decreased from 2.05 to 0.35 Am^-2 in a microbial electrochemical cell. Substantial increase of the Treponema population was observed in the biofilm anode at Eanode=+0.2 V, which reduced intracellular electron-transfer kinetics associated with the maximum specific substrate-utilization rate by a factor of ten. This result suggests that fast EET kinetics can be maintained under dynamic Eanode conditions in a highly conductive biofilm anode as a result of shift of main EET players in the biofilm anode, although Eanode changes can influence IET kinetics. This dataset is associated with the following publication: Dhar, B., H. Ryu, H. Ren, J. Santodomingo, J. Chae, and H. Lee. High Biofilm Conductivity Maintained Despite Anode Potential Changes in a Geobacter-Enriched Biofilm. ChemSusChem. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, GERMANY, 9(24): 3485 –3491, (2016).

Acetylene (C2H2) is a molecule rarely found in nature, with few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs, however we hypothesized that there may be yet unrecognized diversity of acetylenotrophs in nature. In this study, we expanded this diversity by isolating an aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethene (TCE)-contaminated soils undergoing bioremediation. TCE-contaminated soils from the NASA Ames Research Center in California were used to establish soil microcosms with acetylene as the primary carbon substrate and acetylene uptake was tracked over time and reported in T1_soil_microcosm_v2.0.csv. DNA was extracted from soil microcosm samples for microbial community analysis based on 16S rRNA gene sequencing; the resulting operational taxonomic units are presented in T2_soil_OTU_v2.0.csv. Bradyrhizobium sp. strain I71 was isolated from the soil microcosms and acetylene uptake and cell growth data for the isolate over time are shown in T3_soil_isolate_v2.0.csv. Nitrogen fixation assays for the pure culture of Bradyrhizobium sp. strain I71 are reported in T4_N2_fixation_v2.0.csv. Acetylene concentrations and cell densities from acetylenotrophic and heterotrophic growth assays for Bradyrhizobium sp. strain I71 are reported in T5_GrowthCurve_v2.0.csv

These data include raw sequencing data (bacterial 16S and eukaryote 18S rRNA genes) and a summary result table for bacteria classification in an Excel file. This dataset is associated with the following publication: Hwang, J., H. Ryu, K. Rodriguez, S. Fahad, J. SantoDomingo, A. Kushima, and W. Lee. A strategy for power generation from bilgewater using a photosynthetic microalgal fuel cell (MAFC). JOURNAL OF POWER SOURCES. Elsevier Science Ltd, New York, NY, USA, 484: 229222, (2021).

These data are bacterial 16S rRNA sequences and a taxonomic summary table for biofilm samples from the bio-reactors. The data may provide background/supporting information for other researchers who have a similar experimental plan with a microbial electrochemical cell reactor. This dataset is associated with the following publication: Santodomingo, J., H. Lee, B. Dhar, J. An, B. Rittmann, H. Ren, and J. Chae. The Roles of Biofilm Conductivity and Donor Substrate Kinetics in a Mixed-Culture Biofilm Anod. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 50(23): 12799-12807, (2016).

A-3txf_sequence summary.xksx: Abundance of contigs or unique sequences for each biofilm samples from anodes in the MEC reactor Hodon Waterloo final_fasta_working.docx: Raw sequences with their identification numbers RNA S1_MEC.docx: Representative sequences with their ID number and taxonomy. This dataset is associated with the following publication: Santodomingo, J., H. Ryu, B. Dhar, and H. Lee. Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell. JOURNAL OF POWER SOURCES. Elsevier Science Ltd, New York, NY, USA, 331: 315-321, (2016).

Sequence reads (16S rDNA- and 16S rRNA-based) were processed and analyzed using Mothur software. The results presented in the attached Excel file. Also, the other MS word file includes taxonomic summary tables for bacterial communities on biofilms from the MAIFAS reactor as well as the detailed description of Materials & Methods. This dataset is associated with the following publication: Church, J., H. Ryu, A. Sadmani, A. Randall, J. Santodomingo, and W.H. Lee. Multiscale investigation of a symbiotic microalgal-integrated fixed film activated sludge (MAIFAS) process for nutrient removal and photo-oxygenation. Bioresource Technology. Elsevier Online, New York, NY, USA, 268: 128-138, (2018).

Subsurface microbial (biogenic) methane production is an important part of the global carbon cycle and has resulted in natural gas accumulations in many coal beds worldwide. Laboratory experiments indicate coal beds can act as natural geobioreactors and produce additional low carbon renewable natural gas with algal or yeast compounds, yet the effectiveness of these nutrients in situ are unknown. This study uses down-well monitoring methods in combination with deuterated water (99.99% D2O) and a 200-liter injection of 0.1% yeast extract to stimulate and isotopically label newly generated methane. A total dissolved gas pressure sensor was placed down-well into the Flowers-Goodale coal bed at the USGS Birney Test Site in the Powder River Basin, USA, to facilitate long-term real-time gas measurements 641 days pre-injection and for 478 days post-injection. Calculations from isotopic labeling from D2O indicates the methane concentration increased 132% above pre-injection levels 266 days post-injection. This study demonstrates the ability to both isotopically label newly generated methane in situ and monitor increases which has immediate implications for investigating methane generation in other environments.

Presented here is the environmental microbiome study of the International Space Station surfaces. The environmental samples were collected with the polyester wipes from eight different locations in the ISS during two consecutive sampling sessions (three months apart). The specific objective was to unveil the pool of genes for each location during two separate sessions to learn of functional and metabolic diversity of microorganisms in the ISS. The International Space Station (ISS) as a closed built environment has its own environmental microbiome which is shaped by microgravity radiation and limited human presence. The microbial diversity associated with ISS environmental surfaces was investigated during this study. Polyester wipes and contact slides were used for sampling of eight various surface locations on the ISS at different time periods. The samples were retrieved and analyzed immediately upon the return to the Earth (via Soyuz TMA-14M or Dragon capsule from SpaceX). After surface sample collection contact slides containing nutrient media for the growth of bacteria and fungi were incubated at 25 xcb x9aC. The polyester wipes were processed to measure microbial burden (R2A Blood Agar and Potato Dextrose Agar) and recover cultivable bacteria as well as fungi. Subsequently viable microbial burden was assessed using Adenosine Triphosphate (ATP) assay and quantitative polymerase chain reaction (PCR) methods after propidium monoazide (PMA) treatment. The 16S-tag and metagenome analyses were used to elucidate viable microbial diversity. The cultivable bacterial population yield from the polyester wipes was very high (5 to 7-logs) when compared with the contact slides (102 to 103 CFU/m2). The PMA-qPCR analysis showed considerable variation of viable bacterial population (105 to 109 16S rDNA gene copies/m2) among locations sampled. Unlike contact slides polyester wipes cover much larger sample surface (~1 m2) and produce much more reliable results of the microbial diversity of the ISS covering both cultivable and non-cultivable species. The cultivable total and viable microbial diversity was determined utilizing state-of-the art molecular techniques. The implementation of the PMA assay before DNA extraction allowed distinguishing viable microorganisms which is crucial for determining their role to the crew health the ISS maintenance and the general knowledge of the closed environmentally controlled built systems.