On the anaerobic microbial degradation of organosulfonates and of bioplastics

Abstract

In anoxic environments, anaerobic microbial respirations and fermentations are the main processes driving the turnover of compounds, and thus play significant roles in the biogeochemical, e.g., carbon and sulfur cycles in these environments. In my thesis, I used growth experiments, analytical chemistry, and state-of-the-art molecular methods including genomics, transcriptomics, and proteomics to investigate the anaerobic microbial degradation of two groups of compounds, naturally occurring organosulfonates and man-made, but also naturally occurring biopolymers (bioplastics). Organosulfonates are produced by a wide range of organisms from all domains of life, and are therefore ubiquitous in nature. Several microbial pathways have been reported for their mineralization, most of which involve microbial communities. Here, I investigated a microbial community that degraded the organosulfonate sulfoquinovose (SQ). In addition, a pure culture of the human gut pathobiont Bilophila wadsworthia was examined for its ability to respire several other organosulfonates. Finally, I investigated the ability of anaerobic fermenting microbial communities to mineralize the bioplastic poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and other bioplastics, such as long-chain polyesters. By investigating a strictly anaerobic SQ-degrading bacterial consortium, that produced the C2-organosulfonate isethionate as a major product, but also the C3-organosulfonate 2,3-dihydroxypropanesulfonate, I discovered a novel bifurcated degradation pathway in Faecalicatena spp. that combined the known 6 deoxy-6-sulfofructose transketolase and 6 deoxy-6-sulfofructose transaldolase pathways. In a second step, the consortium completely degraded isethionate to hydrogen sulfide (H2S) if an additional electron donor (external H2) was supplied. The isethionate degrader was identified as an Anaerospora sp., that employs the known isethionate-desulfonating glycyl-radical enzyme pathway as described for Bilophila wadsworthia. The results provide the first description of an additional sulfoglycolytic, bifurcated SQ pathway. Furthermore, the study expands the knowledge on sulfidogenic SQ degradation by strictly anaerobic co-cultures, comprising SQ-fermenting bacteria and cross-feeding of the sulfonate intermediate to H2S-producing organisms, a process particularly relevant in gut microbiomes. The human gut pathobiont B. wadsworthia has gained increased attention as a potential contributor to human-gut diseases such as irritable bowel disease and colorectal cancer. This association is thought to be due to increased production of H2S, e.g. from the degradation of organosulfonates, as H2S can damage the intestinal mucus layer and DNA. Since food-derived organosulfonates are diverse, I evaluated additional organosulfonates that may be degraded by the Human Microbiome Project reference strain B. wadsworthia 3.1.6. Here, I can confirm and refine the degradation of known organosulfonates, i.e. sulfoacetate and cysteate. In addition, I can report on new substrates for organosulfonate respiration and on potential degradation pathways used by strain 3.1.6. These novel substrates included sulfopyruvate, N-acetyl taurine and N-methyl taurine. Furthermore, a substrate preference for C2 over C3 organosulfonates was revealed. Finally, a total of 1076 publicly available human fecal metatranscriptomes from 201 individuals were analyzed in order to assess the relevance of described and newly discovered organosulfonates and described electron donors in organosulfonate respiration of B. wadsworthia in situ. Surprisingly, abundant transcripts suggested, sulfolactate as a relevant substrate for organosulfonate respiration in addition to taurine and cysteate in situ, and formate and lactate as the major electron donors. Overall, the study provides a deeper understanding of the metabolic capacity of the model system B. wadsworthia 3.1.6 and the active metabolic features in the human gut. Plastics are part of our everyday lives, but the way in which they are produced and later disposed of is harmful to the environment. Therefore, plastics are being developed that are derived from sustainable sources and that are also biodegradable. Here several plastics that were previously reported to be biodegradable (mostly under oxic conditions) were tested for anaerobic biodegradation: polyethylene terephthalate, PHBV, low-density polyethylene (LDPE), poly-L-lactic acid (PLLA), and two novel polyethylene-like materials, the long-chain polyester-18,18 (PE-18,18) and polyester-12,12 (PE-12,12). The bioplastics were supplied to the cultures as foils. Only the PHBV foil was completely degraded during the incubations. The cultures incubated with PHBV were further investigated for biogas production, community composition, and potential degradation pathways. Rhodocyclaceae and Gammaproteobacteria were identified as the main contributors to PHBV degradation. Metaproteomics indicated that PHBV-degrading bacteria utilized PHB depolymerases and that PHBV-derived carbon was likely stored intracellularly as polyhydroxyalkanoate granules or in the cellular fatty acid pools via fatty acid synthesis, in addition to energy conservation through substrate-level phosphorylation.