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5 Intracellular Mass Transfer and the Effect on Observed Isotope Fractionation

5 Intracellular Mass Transfer and the Effect on Observed Isotope Fractionation

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18  Evaluation of the Microbial Reductive Dehalogenation Reaction …


Fig. 18.2  A microscale mass transfer at microbial systems, as for instance, dissolution, transport trough the membranes, and enzyme-substrate association potentially affect isotope fractionation. Potentially rate-limiting barriers for the PCE were observed to be the outer membrane and

the cytoplasmic membrane. B Furthermore, in case of a cytoplasmic location of the enzyme, the

structure and the properties of RDase are suspected to have an additional effect on mass transfer


limitation observed. Indeed, sorption tests to microbial biomass showed in general

significantly higher sorption of PCE compared to TCE for the gram-negative S.

multivorans, as well as a three times higher sorption capacity of PCE for the gramnegative S. multivorans in comparison to the gram-positive Desulfitobacterium

(Renpenning et al. 2015b).

Although mass transfer limitation masks the real magnitude of the reactionspecific isotope enrichment, information can still be used for evaluation and interpretation intracellular microscale mass transfer processes. These masking effects,

however, are only expected to be observed in cases where the catalytic rate at the

enzyme higher is compared to the rate of mass transfer (Sherwood Lollar et al.

2010; Mancini et al. 2006).

18.5.1 Outer Membrane

Microscale mass transfer-induced isotope masking was reported in several bioavailability studies at low substrate concentration and concentration gradients

(Thullner et al. 2008; Kampara et al. 2008). Effect of rate-limiting mass transfer

on isotope fractionation was demonstrated in several studies using high biomass


J. Renpenning and I. Nijenhuis

concentration (Staal et al. 2007; Templeton et al. 2006; Kampara et al. 2009). The

first evidence for the membrane as a rate-limiting barrier during organohalide respiration was obtained from isotope fractionation studies with growing cells versus crude extracts (Cichocka et al. 2007; Nijenhuis et al. 2005). The destruction

of the cell envelope increased the observed isotope effect significantly. Therefore,

rate-limiting mass transfer at the outer membrane of S. multivorans was considered to be responsible for the observed isotope masking for PCE (Renpenning

et al. 2015b). This demonstrated in addition a correlation between cell composition and variability of isotope fractionation in S. multivorans. The cultivation of

S. multivorans with chlorinated ethenes resulted in a higher saturated fatty acid

content compared to cultivation with fumarate. In addition, the cell surface was

observed to be more hydrophobic during growth with fumarate compared to more

hydrophilic with PCE or TCE. Subsequent dehalogenation experiments confirmed

the contribution of the outer membrane to stronger isotope masking due to the

higher hydrophobicity of the cell surface and higher sorption capacity at the cell


Firmicutes and Chloroflexi, however, do not possess an outer membrane, and

therefore, isotope masking was supposed to be negligible for strains of these

phyla. Still, isotope fractionation was determined to be significantly stronger for

microbial crude extracts in comparison to growing cells for gram-positives, as D.

hafniense and D. restrictus (Renpenning et al. 2015b). Therefore, variability of

isotope fractionation could not be attributed to the outer membrane alone.

18.5.2 Cytoplasmic Membrane

Although S. multivorans RDases are all thought to face to the outside of the cytoplasmic membrane, initial studies on S. multivorans localized the RDase in the

cytoplasm (Neumann et al. 1994). Later studies, however, showed that the cultivation conditions affected the location of the RDase (John et al. 2006). Partial location of the enzyme in the cytoplasm provided further evidence for membranes as

rate-limiting barriers in the dehalogenation reaction, however, also provided evidence for the activity of the enzyme in the cytoplasm (Renpenning et al. 2015b).

Though thus far only investigated for S. multivorans (John et al. 2006), active

cytoplasmic dehalogenase may occur frequently in organohalide-respiring bacteria

during the initial growth, affecting the observed isotope effect. Microscale mass

transfer of chlorinated ethenes in this case will be limited by both, outer membrane

and cytoplasmic membrane. The differences in relative distribution of dehalogenase cytoplasm and periplasm may explain the variability of isotope enrichment

factors observed in different studies as result of differences in growth phase or

conditions, as for instance, isotope enrichment factors for PCE dehalogenated by

the mixed culture KB-1 (−2.6 to −5.5 ‰), Desulfitobacterium strain PCE-S (−5.2

to −8.9 ‰), and Geobacter lovleyi (not significant to −2.3 ‰) (Renpenning et al.

2014; Cichocka et al. 2008; Slater et al. 2001; Nijenhuis et al. 2005).

18  Evaluation of the Microbial Reductive Dehalogenation Reaction …


18.5.3 Rate Limitation at the RDase

The first crystal structure of PceA of S. multivorans was recently published by

Bommer et al. (2014) and revealed an enzyme structure with an active site inside

the core of the protein. To get access to the active site chlorinated hydrocarbons

have to pass a 12 Å long and 3 × 5.5 Å wide hydrophobic channel. The channel forms a restriction filter and is thought to disfavor access for molecules larger

than halogenated ethenes. Similarly to the isotope-masking effect of the outer and

cytoplasmic membranes, Rdh enzymes may restrict the mass transfer for highly

hydrophobic compounds to the active site and enhance isotope masking. Evidence

for rate limitation at the active site of PceA RDase (S. multivorans) was provided

by Renpenning et al. (2014). Using corrinoids, abiotic dehalogenation rates were

observed to be about 10 times faster for PCE versus TCE, while enzyme-catalyzed

dehalogenation rates were similar for both chlorinated ethenes. Therefore, the initial binding and transport of PCE toward the active center may be a rate-limiting

step. Furthermore, dual-element analysis suggested a multistep reaction with different isotope effects of Cl versus C (Renpenning et al. 2014). This can only be

explained by rate limitation if the association of PCE to the hydrophobic channel

exhibits a pronounced isotope effect overlain by the isotope effects of the reaction or if the reaction involves two steps, e.g., binding of the substrate prior to

the dehalogenation at the active center (Fig. 18.2). Experiments with pure corrinoids already indicated that rate-limiting events, such as the dissociation of the

lower ligand (Sect. may have a significant effect on the measured isotope

fractionation. Moreover, the significant Cl isotope effect versus the insignificant

carbon isotope effects during sorption of TCE (Shouakar-Stash et al. 2009) would

suggest strong interaction of PCE with enzyme resulting in overlaying isotope

effects. Therefore, rate limitation at the active site of the enzyme would explain

the overall low isotope fractionation of hydrophobic PCE by several microbial strains capable of dehalogenation, whereas the less hydrophobic TCE was

observed to be not or insignificantly affected.

18.6 Conclusion

Even with some limitations in microbial systems, CSIA is especially valuable to

investigate a reaction without the need for a purified enzyme or crystal structure.

Though CSIA is mainly applied for carbon and partly for chlorine, it helped to

confirm similarity in reaction mechanisms for enzymatic and abiotic reductive

dehalogenation mediated by pure corrinoids (Renpenning et al. 2014; Cretnik

et al. 2013, 2014). Furthermore, CSIA could show that different corrinoids do not

affect the reaction mechanism, as it was previously suggested (Nijenhuis et al.

2005; Yan et al. 2012). Different corrinoids types (DMB versus non-DMB ligand)

were observed to change dual-element isotope fractionation, and differences were


J. Renpenning and I. Nijenhuis

absent after incorporation of corresponding corrinoid types into the PceA RDase

of S. multivorans (Renpenning et al. 2014). These results coincide with the first

published crystal structure from PceA of S. multivorans (Bommer et al. 2014). For

the reaction mechanism, however, preliminary results using dual-element analysis

of carbon and chlorine do suggest a multistep reaction at the enzyme. Moreover,

intracellular microscale mass transfer over membranes and at the enzyme can

strongly affect the observed isotope fractionation as shown for S. multivorans. The

extent of rate limitation is determined by growth conditions affecting cell composition but also by enzyme localization as well as by the substrate properties.

Highest rate limitation can be expected for hydrophobic compounds such as PCE.

Overall, compound-specific isotope fractionation of organohalides remains

a challenging task, though major steps were undertaken to overcome the limitations in isotope analysis of chlorine and hydrogen. Disregarding, CSIA of carbon

and first investigations for chlorine already provided valuable information about

the various steps of organohalide respiration. Therefore, extension of CSIA to a

multielement stable isotope analysis, including carbon, chlorine, and hydrogen may reveal more and more detailed insight into the process of reductive


Acknowledgments  This study was funded by the Deutsche Forschungsgemeinschaft (Research

Unit FOR 1530 NI 1329/1-1).


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