Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system

<div><p>An ecosystem is a community comprising living and nonliving components of the environment. Microbes are ubiquitous elements in each of these components. The dynamics of microbiota formation in an ecosystem is important to elucidate, because how the different components of a system exchange microbes, and how the microbes control ecological processes remain unresolved. In this study, an abalone, <i>Haliotis diversicolor</i>, seed-nursing pond was used as a model system. We first examined changes in bacterial communities during the seedling cultivation of this herbivorous juvenile aquatic invertebrate animal. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to analyze bacterial community dynamics and spatio-temporal interactions of different system components: consumers (abalone), producers (algae or a substrate), and the environment (water). DGGE fingerprints revealed that the developmental stages of abalone influences bacterial communities of both the abalone and substrate. Although the communities in water fluctuated daily, they could be divided into two clusters that coincided with abalone stages, reflecting the transition from larva to juvenile at around day 21. Pyrosequencing showed that the microbiota in the abalone and substrate had more operational taxonomic units in common than that of either with water. The Bray-Curtis similarity index was used to quantify the formation dynamics of microbiota among the various components of the system. The bacterial communities in producers and consumers showed similar changes. These communities were unstable at the beginning and then slowly stabilized over time. The environmental bacterial community was more stable than the bacterial communities in consumers and producers, and may have been the basis for stability in the system. Our research provides insights into the dynamics of microbiota formation in various biotic elements of a system that will contribute to predictive systems modeling.</p></div

Effects of the three bacterial communities on each other in the abalone seed-nursing ecosystem based on a Bray-Curtis similarity percentage (BC%) analysis.

<p>A, Abalone; S, Adherent substrate; W, Water; n − 1, time point prior to “n.” Using the A sample as an example, the microbiome of A is influenced by two spatially (Sn-An and Wn-An), one temporally (An-1-An), and two spatio-temporally (Sn-1-An and Wn-1-An) adjacent samples. Wn-1-An (light blue) indicates the BC_Wn-1-An percentage in a total of five BCs of A; Wn-An (dark blue) indicates the BC_Wn-An; Sn-1-An percentage (light green) indicates the percentage of BC_Sn-1-An; Sn-An (dark green) indicates the percentage of BC_Sn-An; and An-1-An (red) indicates the percentage of BC_An-1-An. This can be repeated for the additional samples. For details, please refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182590#pone.0182590.g001" target="_blank">Fig 1</a> and Material and Methods.</p

Principal component analysis of bacterial communities in abalone seed-nursing ecosystem samples.

<p>A, with water samples; B, without water samples; blue square, water; green circle, adherent substrate; red triangle, abalone; Arabic numerals, sampling days. Results were plotted using Canoco for Windows 4.5, and the 5,000 most abundant operational taxonomic units of the analyzed samples were used in this analysis. Log transformation (Y' = log (Y + 1)).</p

Changes in α-diversity (Shannon-Wiener indexes) of each component in the abalone seed-nursing system over time.

<p>Different lengths of colored bars show different developmental stages of the abalone. Green, trochophore stage (0–2 days); Purple, creeping larva stage (2–4 days); Yellow, peristomial shell larva stage (4–12 days); Red, differentiation stage (12–21 days); Blue, juvenile (> 21 days).</p

Schematic representation of the BC% analysis of the abalone seed-nursing ecosystem.

<p>“A,” “S,” and “W” represent different components of the ecosystem with direct microbial exchanges. Comparisons of bacterial communities were only conducted for two samples that were spatially or temporally adjacent, e.g., An-1&An, Wn-1&An, Sn&An. The microbiome of “An” is mainly influenced by five spatially and temporally adjacent samples: Wn-1, An-1, Sn-1, Wn, and Sn. The influence of “W” or “S” was external and that of “An-1” was internal. When the BC values of “An” are considered 100%, the BC percentage (BC%) reflects the strength of the influence on “An”. BC, Bray-Curtis similarity value; A, Abalone; S, Adherent substrate; W, Water; n − 1, Time point prior to “n.”</p

PCA plots based on bacterial denaturing gradient gel electrophoresis patterns of the three components in the abalone seed-nursing system.

<p>Different colored dots indicate the different developmental stages of the abalone. Green, trochophore stage (0–2 days); Purple, creeping larva stage (2–4 days); Yellow, peristomial shell larva stage (4–12 days); Red, differentiation stage (12–21 days); Blue, juvenile (> 21 days).</p

Common operational taxonomic unit (out) percentages of the three components in the abalone seed-nursing ecosystem samples.

<p>A, Abalone; S, Adherent substrate; W, Water. Unique, unique operational taxonomic units (OTUs) in each sample; AW, SW, and AS, common OTUs in two samples; ASW, common OTUs in all three samples. The numbers of OTUs in each sample type: A, 119,722; S, 64,431; W, 49,217.</p

Ruthenium Ion-Catalyzed Oxidation of Shenfu Coal and Its Residues

Shenfu coal (SFC), its liquefaction residue (R_L), and carbon disulfide (CS₂)/tetrahydrofuran (THF)-inextractable matter (R_E) were subject to ruthenium ion-catalyzed oxidation to understand the differences in structural features among the above three samples. The results suggest that SFC is rich in long-chain arylalkanes and α,ω-diarylalkanes (DAAs) with carbon number of methylene linkage from 2 to 4 and that long-chain arylalkanes and DAAs are reactive toward hydroliquefaction and soluble in a CS₂/THF mixed solvent, whereas highly condensed aromatic species in SFC show poor solubility in the CS₂/THF mixed solvent

Ruthenium Ion-Catalyzed Oxidation of Shenfu Coal and Its Residues

Shenfu coal (SFC), its liquefaction residue (R_L), and carbon disulfide (CS₂)/tetrahydrofuran (THF)-inextractable matter (R_E) were subject to ruthenium ion-catalyzed oxidation to understand the differences in structural features among the above three samples. The results suggest that SFC is rich in long-chain arylalkanes and α,ω-diarylalkanes (DAAs) with carbon number of methylene linkage from 2 to 4 and that long-chain arylalkanes and DAAs are reactive toward hydroliquefaction and soluble in a CS₂/THF mixed solvent, whereas highly condensed aromatic species in SFC show poor solubility in the CS₂/THF mixed solvent