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Ecology of methane consuming bacteria in wetlands (Alleen Engelse tekst)
Background
Next to CO2, CH4 (methane) is the most important greenhouse gas. A large part of the methane emitted to the atmosphere (30-40%) originates from wetland environments (e.g. rice fields, littoral zones of lakes, floodplains, peatlands). The soils and sediments in wetland environments are largely anoxic giving rise to methane formation by methanogenic microbes. However, in the upper part of these soils and sediments or surrounding the roots of wetland plants there is oxygen available. Here methane consuming bacteria degrade the methane by respiring it with oxygen. In this way up to 90% of the methane produced in these habitats is degraded before it can be emitted to the atmosphere. Hence, the methane consuming bacteria play an eminent role in the control of methane in our atmosphere and hence also in our climate. To understand what controls the methane emission globally and what causes the variation therein it is of great importance to have knowledge on the ecology of these fascinating bacteria.
Methane consumers are a very special group of microbes because they only utilize CH4 to generate energy and biomass. Next to this it is a group of bacteria where the phylogeny (taxonomy) is reflected in the natural occurrence and ecology. They also contain specific biomarker molecules (fatty acids) that separate them from other bacteria. These characteristics make these microbes ideal subjects for microbial ecology studies.
We study methane consuming microbes in Floodplains (ESF-NWO, METHECO), in lake sediments and in peat lands. Next to this we also study methane consuming microbes and their role in aquatic food webs after being consumed by protozoa or chironomids.
The central question in studies is: is microbial diversity important for the biogeochemical function they catalyse?
Within these lines of research there are several opportunities for students to take part.
Student Subjects
1: Effect of plant diversity of methane consuming microbes in floodplains
This is part of the METHECO project sponsored by the ESF (European Science Foundation) and NWO (Netherlands Organization for Scientific Research).
This is part of the METHECO project sponsored by the ESF (European Science Foundation) and NWO (Netherlands Organization for Scientific Research).
In microcosm experiments we will test whether plants which are tolerant against flooding or plants which can not cope with flooding affect the methane consuming microbial community with possible consequence s for methane emission from these soils.
2: Re-colonization potential of methane consuming microbes
Also this subject is part of the METHECO project and will focus on the potential of methane consuming microbes to colonise habitats and turn them into a sink for methane. Especially plant roots are thought to be of importance in this respect because the roots transport the bacteria through the soil or sediment. Also these experiments will be carried out microcosm systems.
Also this subject is part of the METHECO project and will focus on the potential of methane consuming microbes to colonise habitats and turn them into a sink for methane. Especially plant roots are thought to be of importance in this respect because the roots transport the bacteria through the soil or sediment. Also these experiments will be carried out microcosm systems.
3: Comparing the active with the inactive methane consuming community
Microbial diversity is mostly assessed by looking at DNA. However, since DNA in soils and sediments is rather stable it will only give information on presence of microbes but not on what they are doing. To elucidate the functional diversity we have to look at RNA or sort the active cells first out of the environment before further analyses. Within the METHECO project a detailed comparison will be made between RNA and DNA based diversity of methane consuming microbes in floodplain soils.
Microbial diversity is mostly assessed by looking at DNA. However, since DNA in soils and sediments is rather stable it will only give information on presence of microbes but not on what they are doing. To elucidate the functional diversity we have to look at RNA or sort the active cells first out of the environment before further analyses. Within the METHECO project a detailed comparison will be made between RNA and DNA based diversity of methane consuming microbes in floodplain soils.
4: Effect of summer flooding on methane consumption in floodplain soils
With climate change it is anticipated that more extreme weather events will occur with extensive periods of drought followed by pulse flooding in summer time. The aim of this subject is to follow the active methane consuming community during such an event. For this a flooding in an experimental plot in a floodplain will be created.
With climate change it is anticipated that more extreme weather events will occur with extensive periods of drought followed by pulse flooding in summer time. The aim of this subject is to follow the active methane consuming community during such an event. For this a flooding in an experimental plot in a floodplain will be created.
5: Effect of nitrogen fertilization on methane-consuming bacteria
Fertilization has been demonstrated to affect methane consuming bacteria. It can be inhibitory to some groups but stimulating to others. The goal of this project is assess what is the mechanism of these effects. When ammonium fertilizers are used nitrite can be formed. In this subject it will be assessed whether various methane consuming bacteria have different sensitivity to nitrite.
Fertilization has been demonstrated to affect methane consuming bacteria. It can be inhibitory to some groups but stimulating to others. The goal of this project is assess what is the mechanism of these effects. When ammonium fertilizers are used nitrite can be formed. In this subject it will be assessed whether various methane consuming bacteria have different sensitivity to nitrite.
6: Effect clay content on activity and diversity of methane consuming bacteria
In studies performed in lake Lauwersmeer, where we assessed the affect of grazing water birds on methane cycling in this lake, the clay content of the sediment was strongly correlated to activity and diversity of methane consuming bacteria. This subject is focused on the elucidating the mechanism behind this. It can be that being attached to clay particles promotes methane consumption but it can also be that more nutrients (e.g. N,P) are available associated to the clay.
In studies performed in lake Lauwersmeer, where we assessed the affect of grazing water birds on methane cycling in this lake, the clay content of the sediment was strongly correlated to activity and diversity of methane consuming bacteria. This subject is focused on the elucidating the mechanism behind this. It can be that being attached to clay particles promotes methane consumption but it can also be that more nutrients (e.g. N,P) are available associated to the clay.
Methods used
In most of the subjects above diversity of methane consuming bacteria will be assessed using molecular biological techniques (PCR, DGGE, cloning, QPCR).
In most of the subjects above diversity of methane consuming bacteria will be assessed using molecular biological techniques (PCR, DGGE, cloning, QPCR).
Methane consumption will be assessed by Gas Chromatography. To couple activity and identity of methane consuming bacteria stable isotopes (13C) will be used that will be traced back in PLFA (phospholipids), DNA or RNA.
Microcosm systems as well as field experiments will be carried out.
Duration
Most of these subjects are suitable for a 6-9 months practical period.
Most of these subjects are suitable for a 6-9 months practical period.
Contact
Information about these subjects can be acquired with Dr. Paul L.E. Bodelier, phone: 31 (0)294 239307, e-mail: p.bodelier@nioo.knaw.nl, web: http://www.nioo.knaw.nl/ppages/pbodelier/, link: http://www.metheco.org/
Information about these subjects can be acquired with Dr. Paul L.E. Bodelier, phone: 31 (0)294 239307, e-mail: p.bodelier@nioo.knaw.nl, web: http://www.nioo.knaw.nl/ppages/pbodelier/, link: http://www.metheco.org/