SAE_SNSP_UVA

NanoSIMS Enabled Approach to Understand Bacterial and Fungal Cellulose Degraders in Soils

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 Obiettivo del progetto (Objective)

'Soils contain the largest pool of carbon on Earth. Cellulose is a major constituent of this carbon since it is a key component of plant structural carbon. Members of the bacteria and fungi are essential for degrading cellulose and thus are essential for cycling carbon. However, the majority of our knowledge on cellulose degradation has been restricted to organisms that we can grow in the laboratory. The reliance on these growth-based methods to understand soil function can be misleading. My previous molecular-based studies, DNA-stable isotope probing (SIP), identified active cellulolytic bacteria and fungi in a collection of different soils, some of which were previously known to degrade cellulose along with other, putatively novel groups. However these studies did neither delaminate the specific bacterial and fungal contributions to cellulose degradation in these soils nor did they reveal systematic differences in the time course of cellulose degradation among these active groups. Furthermore, the putative novel cellulolytic fungal and bacterial groups warrant follow-up work to ascertain if these groups were responsible for the primary breakdown of cellulose and were not only detected as the result of cross feeding. In order to overcome these issues and expand on my previous SIP work, I propose to use SIP with 13C-cellulose in combination with Halogen In Situ Hybridization-Secondary Secondary Ion Mass Spectrometry (HISH-SIMS) to determine and to quantify the in situ contributions of active cellulolytic microorganisms in the soil environment in a previously unachievable manner. The expected scientific outcome include: (1) system-level understanding of the metabolic networks of cellulose degradation; (2) basic understanding of the degree and efficiency cellulose is degraded by microorganisms; (3) improved understanding of primary and secondary responding populations to cellulose; and (4) better characterization of the seemingly unknown groups of cellulose degraders.'

Introduzione (Teaser)

Researchers have advanced a new method to help map soil microbe networks in great detail.

Descrizione progetto (Article)

Soil microbes like bacteria and fungi break down plant matter (cellulose) that is rich in carbon. As such, they play a crucial role in carbon cycling on Earth, yet the factors that influence soil microbial diversity and activity remain poorly understood.

Traditionally, only the tiny proportion of soil microorganisms that can be cultivated in a laboratory were studied to better understand cellulose degradation. But now, thanks to modern molecular techniques, soil samples can be directly investigated.

Some of these techniques have recently been expanded on as part of the EU-funded 'Nanosims enabled approach to understand bacterial and fungal cellulose degraders in soils' (SAE_SNSP_UVA) project. In particular, researchers were able to extract sample components small enough to allow single-cell genome sequencing using advanced instruments.

As a proof-of-concept for their new extraction method, they applied it to the detection of cellulose-degrading microbes from an Austrian beech forest soil. More specifically, they used biogeochemical, molecular and enzymatic studies to characterise different guilds of these microorganisms.

One major finding was that adding glucose to the samples caused a shift in the community to favour bacteria, while adding inorganic nitrogen favoured fungi.

This study has contributed to our knowledge of cellulose degradation and the factors that govern it. As soils contain the largest pool of carbon on Earth, it is important to gain a deeper understanding of its role in the terrestrial carbon cycle.