Phospholipid-Derived Fatty Acids and Quinones as Markers for Bacterial Biomass and Community Structure in Marine Sediments

<div><p>Phospholipid-derived fatty acids (PLFA) and respiratory quinones (RQ) are microbial compounds that have been utilized as biomarkers to quantify bacterial biomass and to characterize microbial community structure in sediments, waters, and soils. While PLFAs have been widely used as quantitative bacterial biomarkers in marine sediments, applications of quinone analysis in marine sediments are very limited. In this study, we investigated the relation between both groups of bacterial biomarkers in a broad range of marine sediments from the intertidal zone to the deep sea. We found a good log-log correlation between concentrations of bacterial PLFA and RQ over several orders of magnitude. This relationship is probably due to metabolic variation in quinone concentrations in bacterial cells in different environments, whereas PLFA concentrations are relatively stable under different conditions. We also found a good agreement in the community structure classifications based on the bacterial PLFAs and RQs. These results strengthen the application of both compounds as quantitative bacterial biomarkers. Moreover, the bacterial PLFA- and RQ profiles revealed a comparable dissimilarity pattern of the sampled sediments, but with a higher level of dissimilarity for the RQs. This means that the quinone method has a higher resolution for resolving differences in bacterial community composition. Combining PLFA and quinone analysis as a complementary method is a good strategy to yield higher resolving power in bacterial community structure.</p></div

Major fingerprints of PLFA and quinone as a marker for different bacterial groups in this study.

<p>In this study, we refer to the different quinones with the following abbreviations: ubiquinone - UQ-<i>n</i>; and menaquinone - MK-<i>n</i>. The number (<i>n</i>) indicates that of the isoprene unit in the side chain of the quinone. Partially hydrogenated MKs were expressed as MK-<i>n</i>(H<i>_x</i>), where <i>x</i> indicates the number of hydrogen atoms saturating the side chain.</p>a<p>PLFA data were modified mainly from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096219#pone.0096219-Boschker1" target="_blank">[23]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096219#pone.0096219-Kaur1" target="_blank">[26]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096219#pone.0096219-Boschker3" target="_blank">[90]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096219#pone.0096219-Ratledge1" target="_blank">[91]</a>.</p>b<p>Quinone data were modified mainly from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096219#pone.0096219-Collins2" target="_blank">[56]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096219#pone.0096219-Yokota1" target="_blank">[92]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096219#pone.0096219-Fujie1" target="_blank">[94]</a>.</p>c<p>Saturated fatty acids.</p>d<p>+, 1–5%; ++, 5–15%; +++, 15–40%; ++++, >40% of total PLFA pool or total quinone pool; *, present in few species; G, a maker found in a broad range of bacteria and algae, and M, a marker can be used specifically as an indicator for specific bacterial group with the phylum.</p

Classification of profiles based on the dissimilarity value matrix data calculated from the mole fractions of a) the bacterial PLFAs and b) the RQs of the sediments.

<p>Abbreviation of each sample indicates the system and other information of the sample (<i>see </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096219#pone-0096219-t001" target="_blank">Table 1</a>). Parentheses in the abbreviation indicate the depth layer at the sampling station.</p

Comparison between bacterial PLFA and RQ concentration in the sediment with different sample sets.

<p>Line indicates trend for the full dataset. The dotted line indicates the 1∶1 relationship.</p

Log/log power regressions and Spearman’s rank coefficients between the bacterial PLFA (nmol gdw⁻¹) and respiratory quinone (RQ) concentrations (nmol gdw⁻¹), and between organic carbon (mg-C gdw⁻¹) and the bacterial PLFA and quinone concentration of individual sample set.

<p>Levels of significance are *<i>P</i><0.05, **<i>P</i><0.01.</p

Cluster analysis of the pattern of differences among samples in the individual bacterial PLFAs and RQs.

<p>The mean mole percentage value indicates the mean mole fraction among all samples.</p

Relationships between: a) organic carbon and RQ/bacterial PLFA ratio in the sediment with different sample sets, b) degradation index and RQ/bacterial PLFA ratio in the Japanese coastal natural- and fish farm sediments.

<p>Relationships between: a) organic carbon and RQ/bacterial PLFA ratio in the sediment with different sample sets, b) degradation index and RQ/bacterial PLFA ratio in the Japanese coastal natural- and fish farm sediments.</p

Comparisons between: a) organic carbon and bacterial PLFA concentration, b) organic carbon and RQ concentration.

<p>Comparisons between: a) organic carbon and bacterial PLFA concentration, b) organic carbon and RQ concentration.</p

Summarized compositions of a) PLFAs and b) quinones with different sample sets.

<p>More than 3 mol% of components to total pool of each PLFAs and RQs were indicated as others. Note that the full range of PLFAs and quinones analyzed is shown here, meaning that this includes both bacteria-specific and non-specific compounds.</p

Sample codes and characteristics.

<p>*Total sampled depth range;</p><p>**<i>n</i>, sample number;</p><p>***OC: organic carbon content,</p><p>****DI: degradation index. Additional information is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096219#pone.0096219.s002" target="_blank">Table S1</a>.</p