Microbial biodiversity and humic matter decomposition in lakes

Starting date
January 1, 2011
Duration (months)
48
Departments
Biotechnology
Managers or local contacts
Pandolfini Tiziana

The complete decomposition of organic matter (biomolecules) into its constituent parts is a fundamental
process of natural ecosystems that has biotechnological applications. Most of the decomposition is carried
out by enzymes produced by microorganisms (bacteria, fungi) in the soil or water. Despite their importance,
little is known of their diversity and of virtually nothing is known of how the interaction of different
microorganisms influences the process. The application of 2nd-generation sequencing technology to
uncultured microorganisms has opened an enormous window of opportunity for discovery of new organisms
and genes of biotechnological importance (e.g. Rusch et al. 2007). It has also provided an incredible tool for
the in-depth study of biodiversity (Gilbert et al 2008). Nonetheless, as the field matures it becomes
increasingly clear that research efforts aimed at biotechnological applications require targeted
metabolic/functional processes, focused questions, and complementary experiments to move beyond the
descriptive stage of the rapidly developing field of metagenomics.
Here we propose a metaOMICS1 approach coupled with targeted enrichments and high-throughput
screening to study the microorganisms and their gene products involved in degradation of humic matter
(HM). Many biotechnological applications rely on enzymes involved in HM degradation. This includes biofuel
processing, fuel cell technology, and novel biotechnological reactions like polycyclic aromatic carbons
hydroxilations to yield chemical building blocks. Producing next-generation biofuels from cellulosic biomass is
particularly relevant, considering the structural similarities between lignocellulosic biomass and HM. Here we
focus on a well-studied lake ecosystem that is rich in HM and fully equipped for ecosystem-level sampling
and experimentation (Lake Grosse Fuchskuhle, Germany). Our project is based on the premise that naturally
occurring microbes synthesize the enzymes required for HM degradation and that a large diversity of
organisms and enzymes are involved in HM decomposition in peat bog lakes and other HM-rich ecosystems
where HM is a primary energy source.
HM is composed of complex and heterogeneous polymers formed by biochemical and chemical reactions
during decay of plant biomass (humification). The vast majority of organic matter in the biospehere is
synthesized by plants during photosynthesis. After death, their biomass is decomposed by fungi and
bacteria, a process that is rapid at first but then reaches a stage where the majority of the remaining material
consists of recalcitrant and structurally complex organic heteropolymers (HM). These are chemically
composed of polysaccharides, phenolic compounds (e.g. lignin, tannins), amino acids, proteins, and other
components (McDonald et al., 2004). Dissolved HM usually comprises 50-80% of the dissolved organic
carbon in aquatic ecosystems, exceeding the organic carbon of living organisms by roughly an order of
magnitude (Wetzel, 2001). HM en route from land to sea is transformed and quenched in freshwater lakes
and streams and these ecosystems therefore play a critical role in this part of the global carbon cycle (Cole et
al., 2007) and can be expected to hold and host efficient mechanisms and microbial assemblages capable of
HM degradation.The rationale for working with laboratory enrichments in a metaOMICs project is two-fold. First is to
functionally understand correlations between microbial diversity and HM compositional changes that we
observe in the natural ecosystem. Second is to explore the rare biosphere that exists in nature at densities
often too low to detect with metaOMICs, but which nevertheless harbors a great deal of novelty.
Enrichments will be established with HM retrieved from Lake Grosse Fuchskuhle as sole source of organic
carbon. This allows us to define environmental conditions and to keep the system in a steady state using
chemostats. Chemical analysis will be applied to define HM compositional changes that occur due to
microbial growth. The increased abundance of the target enzymes (those converting HM) compared with thenatural lake samples, will strongly facilitate their detection and identification by mapping the metaproteome
onto the metagenome of the most active enrichment cultures. Ultimately we envision understanding the
correlation between microbial and chemical diversities by unraveling the key biocatalysts converting HM in
the studied enrichment cultures.
A detailed exploration of the microbial biodiversity would lead not only to the discovery of a large number of
enzymes that are of potential biotechnological importance to the industry, but additionally to an
understanding of how ecosystem processes are carried out and maintained by the diversity of the
community of microorganisms. Positive interactions among species may lead to greater degradation
efficiency, which would not be discovered using more traditional methods of pure cultures. By exploring the
entire community in situ combined with parallel enrichment experiments, we will specifically target how the
composition and biodiversity of the microbial community affects the efficiency of HM processing and also
increase the success of enzyme screening for sustainable biotechnological applications.
In this way we will link the structure and function of microbial communities and test whether biodiversity is
related to ecosystem functioning and ecosystem services. In turn, this will provide critical information on the
diversity required for management that maintains natural diversity in humic-rich lakes.

Sponsors:

7PQ VALUTATI POSITIVAMENTE
Funds: requested

Project participants

Daniela Cecconi
Associate Professor
Barbara Molesini
Assistant Professor
Tiziana Pandolfini
Associate Professor
Research areas involved in the project
Biotechnology & Applied Microbiology

Activities

Research facilities