Publications by authors named "Renxing Liang"

11 Publications

  • Page 1 of 1

Aspartic acid racemization constrains long-term viability and longevity of endospores.

FEMS Microbiol Ecol 2019 10;95(10)

Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.

Certain microorganisms survive long periods of time as endospores to cope with adverse conditions. Since endospores are metabolically inactive, the extent of aspartic acid (Asp) racemization will increase over time and might kill the spores by preventing their germination. Therefore, understanding the relationship between endospore survivability and Asp racemization is important for constraining the long-term survivability and global dispersion of spore-forming bacteria in nature. Geobacillus stearothermophilus was selected as a model organism to investigate racemization kinetics and survivability of its endospores at 65°C, 75°C and 98°C. This study found that the Asp racemization rates of spores and autoclaved spores were similar at all temperatures. The Asp racemization rate of spores was not significantly different from that of vegetative cells at 65°C. The Asp racemization rate of G. stearothermophilus spores was not significantly different from that of Bacillus subtilis spores at 98°C. The viability of spores and vegetative cells decreased dramatically over time, and the mortality of spores correlated exponentially with the degree of racemization (R2 = 0.9). This latter correlation predicts spore half-lives on the order of hundreds of years for temperatures typical of shallow marine sediments, a result consistent with studies about the survivability of thermophilic spores found in these environments.
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http://dx.doi.org/10.1093/femsec/fiz132DOI Listing
October 2019

Community succession in an anaerobic long-chain paraffin-degrading consortium and impact on chemical and electrical microbially influenced iron corrosion.

FEMS Microbiol Ecol 2019 08;95(8)

Department of Microbiology and Plant Biology, Institute for Energy and the Environment, University of Oklahoma, Norman, OK 73019, USA.

Community compositional changes and the corrosion of carbon steel in the presence of different electron donor and acceptor combinations were examined with a methanogenic consortium enriched for its ability to mineralize paraffins. Despite cultivation in the absence of sulfate, metagenomic analysis revealed the persistence of several sulfate-reducing bacterial taxa. Upon sulfate amendment, the consortium was able to couple C28H58 biodegradation with sulfate reduction. Comparative analysis suggested that Desulforhabdus and/or Desulfovibrio likely supplanted methanogens as syntrophic partners needed for C28H58 mineralization. Further enrichment in the absence of a paraffin revealed that the consortium could also utilize carbon steel as a source of electrons. The severity of both general and localized corrosion increased in the presence of sulfate, regardless of the electron donor utilized. With carbon steel as an electron donor, Desulfobulbus dominated in the consortium and electrons from iron accounted for ∼92% of that required for sulfate reduction. An isolated Desulfovibrio spp. was able to extract electrons from iron and accelerate corrosion. Thus, hydrogenotrophic partner microorganisms required for syntrophic paraffin metabolism can be readily substituted depending on the availability of an external electron acceptor and a single paraffin-degrading consortium harbored microbes capable of both chemical and electrical microbially influenced iron corrosion.
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http://dx.doi.org/10.1093/femsec/fiz111DOI Listing
August 2019

Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities.

Elife 2019 06 18;8. Epub 2019 Jun 18.

Department of Geosciences, Princeton University, Princeton, United States.

Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These 'soft tissues' have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil 'soft tissues' differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.
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http://dx.doi.org/10.7554/eLife.46205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581507PMC
June 2019

Predominance of Anaerobic, Spore-Forming Bacteria in Metabolically Active Microbial Communities from Ancient Siberian Permafrost.

Appl Environ Microbiol 2019 08 18;85(15). Epub 2019 Jul 18.

Princeton University, Princeton, New Jersey, USA.

The prevalence of microbial life in permafrost up to several million years (Ma) old has been well documented. However, the long-term survivability, evolution, and metabolic activity of the entombed microbes over this time span remain underexplored. We integrated aspartic acid (Asp) racemization assays with metagenomic sequencing to characterize the microbial activity, phylogenetic diversity, and metabolic functions of indigenous microbial communities across a ∼0.01- to 1.1-Ma chronosequence of continuously frozen permafrost from northeastern Siberia. Although Asp in the older bulk sediments (0.8 to 1.1 Ma) underwent severe racemization relative to that in the youngest sediment (∼0.01 Ma), the much lower d-Asp/l-Asp ratio (0.05 to 0.14) in the separated cells from all samples suggested that indigenous microbial communities were viable and metabolically active in ancient permafrost up to 1.1 Ma. The microbial community in the youngest sediment was the most diverse and was dominated by the phyla and In contrast, microbial diversity decreased dramatically in the older sediments, and anaerobic, spore-forming bacteria within became overwhelmingly dominant. In addition to the enrichment of sporulation-related genes, functional genes involved in anaerobic metabolic pathways such as fermentation, sulfate reduction, and methanogenesis were more abundant in the older sediments. Taken together, the predominance of spore-forming bacteria and associated anaerobic metabolism in the older sediments suggest that a subset of the original indigenous microbial community entrapped in the permafrost survived burial over geological time. Understanding the long-term survivability and associated metabolic traits of microorganisms in ancient permafrost frozen millions of years ago provides a unique window into the burial and preservation processes experienced in general by subsurface microorganisms in sedimentary deposits because of permafrost's hydrological isolation and exceptional DNA preservation. We employed aspartic acid racemization modeling and metagenomics to determine which microbial communities were metabolically active in the 1.1-Ma permafrost from northeastern Siberia. The simultaneous sequencing of extracellular and intracellular genomic DNA provided insight into the metabolic potential distinguishing extinct from extant microorganisms under frozen conditions over this time interval. This in-depth metagenomic sequencing advances our understanding of the microbial diversity and metabolic functions of extant microbiomes from early Pleistocene permafrost. Therefore, these findings extend our knowledge of the survivability of microbes in permafrost from 33,000 years to 1.1 Ma.
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http://dx.doi.org/10.1128/AEM.00560-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6643238PMC
August 2019

Anaerobic biodegradation of biofuels and their impact on the corrosion of a Cu-Ni alloy in marine environments.

Chemosphere 2018 Mar 13;195:427-436. Epub 2017 Dec 13.

Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA. Electronic address:

Fuel biodegradation linked to sulfate reduction can lead to corrosion of the metallic infrastructure in a variety of marine environments. However, the biological stability of emerging biofuels and their potential impact on copper-nickel alloys commonly used in marine systems has not been well documented. Two potential naval biofuels (Camelina-JP5 and Fisher-Tropsch-F76) and their petroleum-derived counterparts (JP5 and F76) were critically assessed in seawater/sediment incubations containing a metal coupon (70/30 Cu-Ni alloy). Relative to a fuel-unamended control (1.2 ± 0.4 μM/d), Camelina-JP5 (86.4 ± 1.6 μM/d) and JP5 (77.6 ± 8.3 μM/d) stimulated much higher rates of sulfate reduction than either FT-F76 (11.4 ± 2.7 μM/d) or F76 (38.4 ± 3.7 μM/d). The general corrosion rate (r = 0.91) and pitting corrosion (r = 0.92) correlated with sulfate loss in these incubations. Despite differences in microbial community structure on the metal or in the aqueous or sediment phases, sulfate reducing bacteria affiliated with Desulfarculaceae and Desulfobacteraceae became predominant upon fuel amendment. The identification of alkylsuccinates and alkylbenzylsuccinates attested to anaerobic metabolism of fuel hydrocarbons. Sequences related to Desulfobulbaceae were highly enriched (34.2-64.8%) on the Cu-Ni metal surface, regardless of whether the incubation received a fuel amendment. These results demonstrate that the anaerobic metabolism of biofuel linked to sulfate reduction can exacerbate the corrosion of Cu-Ni alloys. Given the relative lability of Camelina-JP5, particular precaution should be taken when incorporating this hydroprocessed biofuel into marine environments serviced by a Cu-Ni metallic infrastructure.
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http://dx.doi.org/10.1016/j.chemosphere.2017.12.082DOI Listing
March 2018

Microbial activities in hydrocarbon-laden wastewaters: Impact on diesel fuel stability and the biocorrosion of carbon steel.

J Biotechnol 2017 Aug 21;256:68-75. Epub 2017 Feb 21.

Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA. Electronic address:

Anaerobic hydrocarbon biodegradation not only diminishes fuel quality, but also exacerbates the biocorrosion of the metallic infrastructure. While successional events in marine microbial ecosystems impacted by petroleum are well documented, far less is known about the response of communities chronically exposed to hydrocarbons. Shipboard oily wastewater was used to assess the biotransformation of different diesel fuels and their propensity to impact carbon steel corrosion. When amended with sulfate and an F76 military diesel fuel, the sulfate removal rate in the assay mixtures was elevated (26.8μM/d) relative to incubations receiving a hydroprocessed biofuel (16.1μM/d) or a fuel-unamended control (17.8μM/d). Microbial community analysis revealed the predominance of Anaerolineae and Deltaproteobacteria in F76-amended incubations, in contrast to the Beta- and Gammaproteobacteria in the original wastewater. The dominant Smithella-like sequences suggested the potential for syntrophic hydrocarbon metabolism. The general corrosion rate was relatively low (0.83 - 1.29±0.12mpy) and independent of the particular fuel, but pitting corrosion was more pronounced in F76-amended incubations. Desulfovibrionaceae constituted 50-77% of the sessile organisms on carbon steel coupons. Thus, chronically exposed microflora in oily wastewater were differentially acclimated to the syntrophic metabolism of traditional hydrocarbons but tended to resist isoalkane-laden biofuels.
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http://dx.doi.org/10.1016/j.jbiotec.2017.02.021DOI Listing
August 2017

Metabolic Capability of a Predominant Halanaerobium sp. in Hydraulically Fractured Gas Wells and Its Implication in Pipeline Corrosion.

Front Microbiol 2016 22;7:988. Epub 2016 Jun 22.

Department of Microbiology and Plant Biology and OU Biocorrosion Center, University of Oklahoma Norman, OK, USA.

Microbial activity associated with produced water from hydraulic fracturing operations can lead to gas souring and corrosion of carbon-steel equipment. We examined the microbial ecology of produced water and the prospective role of the prevalent microorganisms in corrosion in a gas production field in the Barnett Shale. The microbial community was mainly composed of halophilic, sulfidogenic bacteria within the order Halanaerobiales, which reflected the geochemical conditions of highly saline water containing sulfur species (S2O3 (2-), SO4 (2-), and HS(-)). A predominant, halophilic bacterium (strain DL-01) was subsequently isolated and identified as belonging to the genus Halanaerobium. The isolate could degrade guar gum, a polysaccharide polymer used in fracture fluids, to produce acetate and sulfide in a 10% NaCl medium at 37°C when thiosulfate was available. To mitigate potential deleterious effects of sulfide and acetate, a quaternary ammonium compound was found to be an efficient biocide in inhibiting the growth and metabolic activity of strain DL-01 relative to glutaraldehyde and tetrakis (hydroxymethyl) phosphonium sulfate. Collectively, our findings suggest that predominant halophiles associated with unconventional shale gas extraction could proliferate and produce sulfide and acetate from the metabolism of polysaccharides used in hydraulic fracturing fluids. These metabolic products might be returned to the surface and transported in pipelines to cause pitting corrosion in downstream infrastructure.
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http://dx.doi.org/10.3389/fmicb.2016.00988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4916785PMC
July 2016

Anaerobic Biodegradation of Alternative Fuels and Associated Biocorrosion of Carbon Steel in Marine Environments.

Environ Sci Technol 2016 05 22;50(9):4844-53. Epub 2016 Apr 22.

Department of Microbiology and Plant Biology and OU Biocorrosion Center, University of Oklahoma , Norman, Oklahoma 73069, United States.

Fuels that biodegrade too easily can exacerbate through-wall pitting corrosion of pipelines and tanks and result in unintentional environmental releases. We tested the biological stability of two emerging naval biofuels (camelina-JP5 and Fischer-Tropsch-F76) and their potential to exacerbate carbon steel corrosion in seawater incubations with and without a hydrocarbon-degrading sulfate-reducing bacterium. The inclusion of sediment or the positive control bacterium in the incubations stimulated a similar pattern of sulfate reduction with different inocula. However, the highest rates of sulfate reduction were found in incubations amended with camelina-JP5 [(57.2 ± 2.2)-(80.8 ± 8.1) μM/day] or its blend with petroleum-JP5 (76.7 ± 2.4 μM/day). The detection of a suite of metabolites only in the fuel-amended incubations confirmed that alkylated benzene hydrocarbons were metabolized via known anaerobic mechanisms. Most importantly, general (r(2) = 0.73) and pitting (r(2) = 0.69) corrosion were positively correlated with sulfate loss in the incubations. Thus, the anaerobic biodegradation of labile fuel components coupled with sulfate respiration greatly contributed to the biocorrosion of carbon steel. While all fuels were susceptible to anaerobic metabolism, special attention should be given to camelina-JP5 biofuel due to its relatively rapid biodegradation. We recommend that this biofuel be used with caution and that whenever possible extended storage periods should be avoided.
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http://dx.doi.org/10.1021/acs.est.5b06388DOI Listing
May 2016

Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines.

Front Microbiol 2014 6;5:89. Epub 2014 Mar 6.

Department of Microbiology and Plant Biology, OU Biocorrosion Center, University of Oklahoma Norman, OK, USA.

Thermophilic sulfide-producing microorganisms from an oil pipeline network were enumerated with different sulfur oxyanions as electron acceptors at 55°C. Most-probable number (MPN) analysis showed that thiosulfate-reducing bacteria were the most numerous sulfidogenic microorganisms in pipeline inspection gauge (PIG) scrapings. Thiosulfate-reducing and methanogenic enrichments were obtained from the MPN cultures that were able to use yeast extract as the electron donor. Molecular analysis revealed that both enrichments harbored the same dominant bacterium, which belonged to the genus Anaerobaculum. The dominant archaeon in the methanogenic enrichment was affiliated with the genus Methanothermobacter. With yeast extract as the electron donor, the general corrosion rate by the thiosulfate-reducing enrichment (8.43 ± 1.40 milli-inch per year, abbreviated as mpy) was about 5.5 times greater than the abiotic control (1.49 ± 0.15 mpy), while the comparable measures for the methanogenic culture were 2.03 ± 0.49 mpy and 0.62 ± 0.07 mpy, respectively. Total iron analysis in the cultures largely accounted for the mass loss of iron measured in the weight loss determinations. Profilometry analysis of polished steel coupons incubated in the presence of the thiosulfate-reducing enrichment revealed 59 pits over an area of 71.16 mm(2), while only 6 pits were evident in the corresponding methanogenic incubations. The results show the importance of thiosulfate-utilizing, sulfide-producing fermentative bacteria such as Anaerobaculum sp. in the corrosion of carbon steel, but also suggest that Anaerobaculum sp. are of far less concern when growing syntrophically with methanogens.
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http://dx.doi.org/10.3389/fmicb.2014.00089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944610PMC
March 2014

Complete degradation of di-n-octyl phthalate by biochemical cooperation between Gordonia sp. strain JDC-2 and Arthrobacter sp. strain JDC-32 isolated from activated sludge.

J Hazard Mater 2010 Apr 10;176(1-3):262-8. Epub 2009 Nov 10.

Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China.

Two bacterial strains were isolated from activated sludge using mixtures of phthalic acid esters (PAEs) as the sole source of carbon and energy. One of the isolates was identified as Gordonia sp. strain JDC-2 and the other as Arthrobacter sp. strain JDC-32, mainly through 16S rRNA gene sequence analysis. Gordonia sp. strain JDC-2 rapidly degraded di-n-octyl phthalate (DOP) into phthalic acid (PA), which accumulated in the culture medium. Arthrobacter sp. strain JDC-32 degraded PA but not DOP. The co-culture of Gordonia sp. strain JDC-2 and Arthrobacter sp. strain JDC-32 degraded DOP completely by overcoming the degradative limitations of each species alone. The biochemical pathway of DOP degradation by Gordonia sp. strain JDC-2 was proposed based on the identified degradation intermediates. The results suggest that DOP is completely degraded by the biochemical cooperation of different microorganisms isolated from activated sludge.
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http://dx.doi.org/10.1016/j.jhazmat.2009.11.022DOI Listing
April 2010

Genetic diversity of phthalic acid esters-degrading bacteria isolated from different geographical regions of China.

Antonie Van Leeuwenhoek 2010 Jan 29;97(1):79-89. Epub 2009 Oct 29.

Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, 410083 Changsha, People's Republic of China.

Thirty-two strains of phthalic acid ester (PAEs)-degrading bacteria were isolated from thirteen geographically diverse sites by enrichment using mixtures of PAEs as the sole source of carbon and energy. Sequence analyses of the 16S rRNA gene indicated that these isolates were from six genera (Arthrobacter, Gordonia, Rhodococcus, Acinetobacter, Pseudomonas, and Delftia). To evaluate the genetic diversity among them, the molecular typing method rep-PCR with primers based on enterobacterial repetitive intergenic consensus, repetitive extragenic palindromes, and BOXAIR sequences was performed. Strain-specific and unique genotypic fingerprints were distinguished for most of these isolates. In addition, utilization of various PAEs and the central intermediate phthalic acid by representative isolates suggested inter-isolate differences in the substrate utilization and degradation pathways. Furthermore, HPLC analysis showed that the rate of dimethyl phthalate degradation varied from 48.32 to 100% between strains. These results suggest a high level of genetic diversity among PAEs-degrading bacteria in the natural environment and their great potential to clean up phthalates-contaminated environments.
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http://dx.doi.org/10.1007/s10482-009-9390-zDOI Listing
January 2010