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Microbial Degradation of Chemical Compounds Used in Onshore Gas Production in the SE of South Australia

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Microbial Degradation of Chemical Compounds Used in Onshore Gas Production in the SE of South Australia Australia’s National Science Agency Microbial degradation of chemical compounds used in onshore gas production in the SE of South Australia GISERA W.15 Nai Tran‐Dinh, Tania J Vergara, Richard Schinteie, Carla Mariani, Paul Greenfield and David J Midgley Report number EP196935 27 September 2019 GISERA CSIRO Energy ISBN (print): 978‐1‐4863‐1411‐9 ISBN (online): 978‐1‐4863‐1412‐6 Citation Tran‐Dinh N, Vergara TJ, Schinteie R, Mariani C & Midgley DJ (2019) Microbial degradation of chemical compounds used in onshore gas production in the SE of South Australia. CSIRO, Australia. Copyright © Commonwealth Scientific and Industrial Research Organisation 2019. To the extent permitted by law, all rights are reserved and no part of this publication covered by copyright may be reproduced or copied in any form or by any means except with the written permission of CSIRO. Important disclaimer CSIRO advises that the information contained in this publication comprises general statements based on scientific research. The reader is advised and needs to be aware that such information may be incomplete or unable to be used in any specific situation. No reliance or actions must therefore be made on that information without seeking prior expert professional, scientific and technical advice. To the extent permitted by law, CSIRO (including its employees and consultants) excludes all liability to any person for any consequences, including but not limited to all losses, damages, costs, expenses and any other compensation, arising directly or indirectly from using this publication (in part or in whole) and any information or material contained in it. CSIRO is committed to providing web accessible content wherever possible. If you are having difficulties with accessing this document please contact [email protected]. Microbial degradation of chemical compounds used in onshore gas production in the SE of South Australia | i Contents Acknowledgments ....................................................................................................................... vii Executive summary .................................................................................................................... viii Key findings .................................................................................................................... viii 1 Introduction .................................................................................................................... 11 Project goals and summary ................................................................................ 11 Chemicals associated with conventional onshore gas activities ......................... 11 Classification of microorganisms and taxonomic schemes ................................ 15 Soil microbiology ................................................................................................ 18 Aquifer microbiology .......................................................................................... 19 Soils and aquifers of the Penola region, South Australia .................................... 20 Experimental design ........................................................................................... 21 Chemicals used in this study .............................................................................. 24 2 Aims ........................................................................................................................... 27 3 Methods .......................................................................................................................... 28 Task 1 ................................................................................................................. 28 Task 2 ................................................................................................................. 28 Task 3, 4 and 5 ................................................................................................... 33 4 Results ........................................................................................................................... 46 Soil and aquifer physicochemistry ..................................................................... 46 Measured degradation of chemical compounds ................................................ 54 Soil mimicking agar single compound degradation trials ................................... 59 Identification of fungal taxa that degrade target chemicals............................... 63 Identification of prokaryotic taxa that degrade target chemicals ...................... 79 Effect of chemical treatments on soil microbiomes and identification of indicator taxa .................................................................................................................. 93 Effect of chemical treatments on aquifer microbiomes and identification of indicator taxa ................................................................................................................ 113 5 Discussion ..................................................................................................................... 124 Acetic Acid ....................................................................................................... 128 Isothiazolinone biocides ................................................................................... 129 Ethanol, isopropanol and methanol ................................................................. 129 2‐aminoethanol................................................................................................ 131 Aliphatic‐type compounds – eicosane, pristane, 2‐ethylhexanol and polyacrylamide .............................................................................................................. 132 Glycols – ethylene, propylene glycols and 2‐butoxyethanol ............................ 134 Bronopol .......................................................................................................... 135 c12 alcohol ethoxylate ..................................................................................... 136 Diethylene glycol ethyl ether ........................................................................... 136 Polyoxypropylene diamine ............................................................................... 137 Triethanolamine ............................................................................................... 137 Xanthan gum .................................................................................................... 138 Glyoxal, glutaraldehyde and Hexahydro‐1,3,5‐tris (2‐hydroxyethyl)‐sym‐triazine ......................................................................................................................... 139 Aromatic compounds – naphthalene and o‐cresol .......................................... 140 d‐limonene ....................................................................................................... 141 Adsorption vs microbial degradation ............................................................... 142 Conceptual model ............................................................................................ 143 6 Recommendations ........................................................................................................ 145 Chemical analyses ............................................................................................ 147 Sequencing data ............................................................................................... 158 Glossary 159 References 161 ii Figures Figure 1‐1: A phylogenetic tree of life. ........................................................................................ 16 Figure 1‐2: Examples of taxonomic lineages for groups from the three domains of life. ............ 17 Figure 1‐3: Schematic representation of bacterial and fungal ribosomal gene regions. Variable regions of ribosomal genes are labelled (V1‐9 in bacteria and ITS1 and ITS2 in fungi). .............. 18 Figure 1‐4: Indicative cross‐section in the onshore Otway Basin, showing major stratigraphy and location of hydrocarbon targets. ................................................................................................. 21 Figure 1‐5: Geographic location of sampling. Copyright ©Google Maps 2019. .......................... 22 Figure 1‐6: Schematic of workflow for onshore gas production chemical compound testing. .... 23 Figure 1‐7: Structures of chemicals used in this project .............................................................. 26 Figure 3‐1: Sampling locations in Penola, South Australia. Copyright ©Google Maps 2019. ...... 29 Figure 3‐2: Showing microcosms (with loose lids) stored in snap‐lock, polypropylene containers with open vessels of a saturated NH4NO3 for humidity. ............................................................. 34 Figure 3‐3: A schematic of the artificial chimeric amplicon used in the present study. .............. 42 Figure 3‐4: PCR primers used in the present study. .................................................................... 43 Figure 4‐1: Compound concentration measurements in various treatments over time (34‐36 days of incubation) for acetic acid. See full description in caption of Figure 4‐2. ....................... 55 Figure 4‐2: Compound concentration measurements in various treatments over time (34‐36 days of incubation). ..................................................................................................................... 56 Figure 4‐3: Anomalous compound concentration measurements
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