Abstract
The microbiome consists of a diverse range of interacting micro-organisms co-evolved with a specific habitat or a host, such as ruminant animals and pastoral plants. Across pastoral farm habitats, microbiomes are involved in many essential ecological services, such as nitrogen fixation, fibre degradation, and organic matter decomposition. Those ecological processes contribute to a complete nutrient cycle and energy flow, providing a foundation to a pastoral farm ecosystem. Therefore, improving pastoral farming production while reducing its environmental impact is dependent on our understanding of linking specific ecological functions with the responsible organism, the underlying mechanisms, and how those microbiomes react to disturbances. Here we investigated the dynamics of pastoral farm microbiomes either within a microbial community (i.e. the rumen microbiome) or across multiple habitats.
Ruminant livestock is the largest source of anthropogenic methane emissions globally. Methanogenic archaea are the main contributors to these emissions, primarily using molecular hydrogen and carbon dioxide. In this work, we investigated the mechanism of hydrogen competition using a simplified rumen microbial community consisting of a hydrogenogenic fermenter (Ruminococcus albus 7), a common fumarate reducer (i.e. Selenomonas subsp. ruminantium lactilytica PC 18) and a methanogenic archaeon (Methanobrevibacter ruminantium M1). The gas chromatography measures of methane and hydrogen gases revealed that fumarate addition with the presence of fumarate reducers drastically reduced CH4 production. The volatile fatty acids measures showed that fumarate reduction reduced CH4 production through H2 competition. However, the metatranscriptomic analyses suggested that H2 utilisation could be affected by many metabolic pathways, such as fumarate hydration.
Given that the microbial interactions (e.g. H2 competition) within the rumen would affect the microbial community function, and microbiomes across pastoral farm habitats are linked through nutrient cycles and energy flows, changes in the microbiome of one habitat would potentially affect microbiomes of nearby habitats (defined as the knock-on effects). However, relationships between microbial communities and critical variables across ecological habitats are frequently studied in isolation. Therefore, we examined how pastoral farm microbiomes respond to soil nitrogen treatment across habitats (rumen, faecal, white clover leaf, white clover root, ryegrass leaf, and ryegrass root). As measured by amplicon and metagenomic sequencing, nitrogen treatment had no impact on microbiome structure, composition, or metabolic potential but altered soil and the neighbouring microbiome networks and the abundance or metabolic potential in individual microbial members in soil and nearby habitats.
Together, these investigations reveal the relationships between micro-organisms within a microbial community and between microbiomes across nearby habitats. In addition, it supports the concept of knock-on effects in a multi-habitat pastoral farm ecosystem and implies the challenges in developing or conducting agricultural practices in the future.