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In the current era of precision oncology, it is widely acknowledged that CRC is a heterogeneous disease entity. Tumor location (right- or left-sided colon cancer or rectal cancer) is a crucial factor in determining disease progression as well as prognosis and influences disease management. In the last decade, numerous works have reported that the microbiome is an important element of CRC carcinogenesis, progression and therapy response. Owing to the heterogeneous nature of microbiomes, the findings of these studies were inconsistent. The majority of the studies combined colon cancer (CC) and rectal cancer (RC) samples as CRC for analysis. Furthermore, the small intestine, as the major site for immune surveillance in the gut, is understudied compared to the colon. Thus, the CRC heterogeneity puzzle is far from being solved, and more research is necessary for prospective trials that separately investigate CC and RC. Our prospective study aimed to map the colon cancer landscape using 16S rRNA amplicon sequencing in biopsy samples from the terminal ileum, healthy colon tissue, healthy rectal tissue and tumor tissue as well as in preoperative and postoperative stool samples of 41 patients. While fecal samples provide a good approximation of the average gut microbiome composition, mucosal biopsies allow for detecting subtle variations in local microbial communities. In particular, the small bowel microbiome has remained poorly characterized, mainly because of sampling difficulties. Our analysis revealed the following: (i) right- and left-sided colon cancers harbor distinct and diverse microbiomes, (ii) the tumor microbiome leads to a more consistent cancer-defined microbiome between locations and reveals a tumor microbiome–ileal microbiome association, (iii) the stool only partly reflects the microbiome landscape in patients with CC, and (iv) mechanical bowel preparation and perioperative antibiotics together with surgery result in major changes in the stool microbiome, characterized by a significant increase in the abundance of potentially pathogenic bacteria, such as Enterococcus. Collectively, our results provide new and valuable insights into the complex microbiome landscape in patients with colon cancer.
Methane (CH4) is a potent greenhouse gas with rising atmospheric concentrations.
Microorganisms are essential players in the global methane cycle. In fact, the largest part of methane emissions derives from microbial production by methanogenic Archaea (methanogens). Microorganisms do not only produce methane: methanotrophs can also oxidize the methane produced by methanogens. In addition, soil methanotrophs are the only biological methane sink, oxidizing up to 30-40 Tg of this potent greenhouse gas per year worldwide.
However, intensified management of grasslands and forests may reduce the methane sink capacity of soils.
In general, the interaction of methanogens and methanotrophs determines whether a soil is a source or a sink for methane. It is, therefore, crucial to understand the microbial part of the methane cycle and which factors influence the abundance and activity of methane-cycling microbes. However, capturing the soil microbiome's abundances, activity, and identity is
challenging. There are numerous target molecules and myriad methods, each with certain
limitations. Linking microbial markers to methane fluxes is therefore challenging. This thesis aimed to understand how methane-cycling microbes in the soil are related to soil methane fluxes and how soil characteristics and human activity influence them.
The first publication investigated the biotic and abiotic drivers of the atmospheric methane sink of soils. It assessed the influence of grassland land-use intensity (150 sites) and forest management type (149 sites) on potential atmospheric methane oxidation rates (PMORs) and the abundance and diversity of CH4-oxidizing bacteria (MOB) with qPCR in topsoils of three temperate regions in Germany. PMORs measured in microcosms under defined conditions were approximately twice as high in forest than in grassland soils. High land-use intensity of grasslands negatively affected PMORs (−40%) in almost all regions. Among the different aspects of land-use intensity, fertilization had the most adverse effect reducing PMORs by 20%.
In contrast, forest management did not affect PMORs in forest soils. Upland soil cluster (USC)α was the dominant group of MOBs in the forests. In contrast, USCγ was absent in more than half of the forest soils but present in almost all grassland soils. USCα abundance had a direct positive effect on PMOR in forests, while in grasslands, USCα and USCγ abundance affected PMOR positively with a more pronounced contribution of USCγ than USCα.
In the second publication, we used quantitative metatranscriptomics to link methane-cycling microbiomes to net surface methane fluxes throughout a year in two grassland soils. Methane fluxes were highly dynamic: both soils were net methane sources in autumn and winter and net methane sinks in spring and summer. Correspondingly, methanogen mRNA abundances per
gram soil correlated well with methane fluxes. Methanotroph to methanogen mRNA ratios were higher in spring and summer when the soils acted as net methane sinks. Furthermore, methane uptake was associated with an increased proportion of USCα and γ pmoA and pmoA2 transcripts. High methanotroph to methanogen ratios would indicate methane sink properties.
Our study links the seasonal transcriptional dynamics of methane-cycling soil microbiomes for the first time to gas fluxes in situ. It suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes.
We conclude that reduction in grassland land-use intensity and afforestation can potentially increase the methane sink function of soils and that different parameters determine the microbial methane sink in forest and grassland soils. Furthermore, this thesis suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes. Methanogen transcript abundance may be used as a proxy for changes in net surface methane emissions from grassland soils.