World Journal of Microbiology and Biotechnology, 8 ($up01ement 1), 117-119
A view on microbial ecology A. Kjoller
There are few occasions where a wider look at the development of research directions is needed. It is a challenge, however, to define one's own place in the research spectrum and attempt to predict some of the new topics to be covered in coming years. Microbial ecology is a rather new discipline within microbiology dealing with the physiology and interactions between microorganisms participating in the biogeochemical processes in the ecosystems. The research in microbial ecology at our laboratory in the Department of General Microbiology, University of Copenhagen has been focused on the ecological role of microorganisms during decomposition of organic matter in deciduous forests. The research has been concentrated on three main topics: denitrification, the role of microfungi and bacteria during decomposition of the litter and anaerobic decomposition of organic matter. The denitrification studies have included determination of the number of organisms, isolation and identification, and measurements of nitrogen (N20) output in situ and from manipulated samples in the laboratory. Microfungi (and bacteria) were enumerated and isolated from leaves' during the 6 to 7 months decomposition period, and the isolates were tested to determine their potential enzymatic capability. The physiology and ecology of anaerobic bacteria included studies of the interactions between sulphatereducing, methane-producing and denitrifying bacteria and the importance of variations in different environmental factors. Even though microorganisms, e.g. bacteria and fungi, have been isolated and studied also in in-situ experiments in natural environments, still more knowledge of occurrence, growth and role in decomposition processes and nitrogen turnover in different ecosystems is needed. It is considered important to study these processes in nature and also to extend the study of the physiology and ecology of microorganisms from natural environments to stressed environments under varying pollution conditions or other A. Kjeller is at the Department of General Microbiology, University of Copenhagen, Solvgade 83 H, DK-1307 Copenhagen K, Denmark.
man-made influence. The changes in and the functional role of the microbial populations during decomposition of forest litter have been investigated during recent years. A continuation of these activities could be possible in a proposed IUBS/IUMS programme (Functional microbial diversity in terrestrial ecosystems). In the proposal the effect of air pollution, acid rain and other environmental disturbances would be included. Another future approach is to continue the in-situ measurements of denitrifying activity in different types of beech forests in which soil pH varies from 4.5 to 6.9. An European network is established between researchers with the aim to examine denitriflcation in different forests in Europe. In this way estimates of nitrogen release from the European woodland ecosystems can be calculated. The previous decomposition and nitrogen turnover projects have been supported by the University of Copenhagen. The future collaboration with other European countries will be granted by the EEC. There is increasing interest for measurements of nitrogen gases and methane escaping to the atmosphere and for environments where these gases are produced. A large international programme, IGBP (International GeosphereBiosphere Programme), has been initiated, and one of the proposed core projects is global change and terrestrial ecosystems. Our future research projects on denitrification and terminal anaerobic carbon decomposition will contribute to this international programme. It is hoped to initiate research in new areas, besides continuing the above-mentioned decomposition and process studies. It is considered vital to take advantage of the new methods offered through the developments in molecular biology and adopt methods for determination of biomass and activity and use new principles for identification of microorganisms. A governmental biotechnology programme was initiated 3 years ago and the Department of General Microbiology hosts the leadership of a centre for environmental biotechnology. Most of the following research areas are included in this programme or are proposed to constitute the basis for a continuation of the centre. The new centre is formed as a centre for the study
9 1992 Rapid Communications of Oxford Ltd World Journal of Microbiology and Biolechnology, Vol 8 5upplemen~ I 9 I992
117
A. Kjo]ler of microbial ecology including environmental and molecular microbial ecology projects.
Microbial Differentiation and Growth Rates in Nature Microorganisms, bacteria and fungi are known to survive and even grow under very unfavourable conditions, e.g. very low nutrient concentrations, in the environment. Some bacteria are obligate oligotrophs, inhibited by high nutrient concentrations, in contrast to fungi which probably are always able to grow at both high and low nutrient concentrations. The importance of oligotrophic growth conditions for the activity of microfungi is unknown and will be investigated with isolates from natural environments. The concentration of nutrients has been shown to influence both growth rate and morphology of the colony. The ability of the individual strains in a population to adapt to different and varying environmental conditions also needs more research. Combinations of ecological, genetical and molecular methods could be used. More information on stress-induced genes in laboratory strains and in strains isolated from their natural habitat would be of interest. Growth rates of bacteria and fungi in natural environments have been very difficult to determine using traditional methods. By innovation of extraction methods and determination of specific cell components it would be possible to measure and estimate growth rate and growth state of the cells in situ.
Degradation of Organic Compounds The previous studies of processes and the role of microorganisms in decomposition of natural organic matter will be continued. Furthermore, degradation studies of man-made organic compounds (xenobiotics) will be intensified, including the importance of interactions between populations of microorganisms, and the environmental factors determining the degrading activity. Physiological characterization of the microbial populations or single strains able to decompose certain xenobiotic compounds is important as is determination of the metabolic pathways during aerobic or anaerobic conditions. Analysis of metabolic activities is necessary before trying to optimize a degradation process. Genetic characterization of strains with specific degradation ability is a necessary basis for future genetic manipulation.
Molecular Microbial Ecology Use of methods from molecular microbiology in microbial ecology will be intensified in the future. Genetic
I 18
World Journal of Microbiology and Biotechnology, Vol 8 Supplement I 9 I992
manipulation directed towards development of new strains with specific abilities, use of markers, identification of bacteria with immuno-techniques, development of new probes, investigation of plasmid transfer in the natural environment, are some of the specific topics for future research. Deliberate release of genetically manipulated microorganisms (GEMs) to nature (e.g. soil) is not permitted yet. The effect of a massive release of microorganisms on natural ecosystems is unknown, and before any permission is issued, investigation of establishment and survival in relevant niches of the GEM to be released will be required. A complex of factors determines the establishment and proliferation of GEMs released to nature including temperature, oxygen, redox, pH, salinity conditions, special nutrient requirement, resistance to antibiotics, conversion of complex organic substances, etc. It is also important to assess the role of the introduced microorganisms in functional key processes in the ecosystem (e.g. hydrolysis of lignin and cellulose, oxidation of ammonia, and reduction of nitrate), and how the organisms may influence and change the structure of the original population. Studies of these cgmplex ecological features have been initiated, and will be continued. Another trend in molecular microbial ecology is the evaluation of gene transfers in nature. It is known from studies of antibiotic resistance in bacteria that gene transfer takes place between unrelated microorganisms, and that identical antibiotic resistance can be found in a wide variety of bacteria. The future aim is to investigate the dispersal of genes in natural ecosystems using resistance genes as model for the dispersal without selective advantages for the host. This project has obtained support from The Nordic Council of Ministers included in a larger programme concerning the environmental risk by deliberate release of genetic manipulated microorganisms. Other projects have been initiated at the University of Bergen, Norway; Helsinki, Finland and G6teborg, Sweden. Other research projects in microbial ecology in Denmark include the following main subjects and tendencies. (1) Microscale studies of the microbial nitrogen cycling associated with the organic particle fraction in the soil is emphasized. Innovation and adaption of new techniques are needed for the study of microbial populations and processes in undisturbed soil samples or in the rhizosphere. A variety of methods are already in use but methods employing molecular biology are of interest, and a collaboration between molecular biologists and microbial ecologists has been initiated. (2) Microbial processes in oxic and anoxic gradient environments. Processes and population studies in sediments and biofilm will be investigated using microelectrodes and probe techniques to evaluate the regulation of aerobic and anaerobic decomposition of organic matter and sulphur
Microbial ecology in Denmark compounds, oxidation of methane, and further to determine the occurrence and zonation of the bacterial populations. (3) Microbial interactions and regulation of the microbial activity during strict anaerobic turnover of organic matter and man-made (xenobiotic) compounds. Facilities for anaerobic cultivation of bacteria (and fungi) are available in several laboratories and new results of the physiology of anaerobic organisms will emerge and may be used for bioremediation purposes. The importance of varying environmental factors on decomposition processes and microbial interactions, and determination of the kinetics during decomposition of xenobiotic compounds are some of the subjects to be investigated during the following years. Molecular methods will be applied to detect and identify important groups of anaerobic bacteria. Physiological and genetic characterization of xenobiotic decomposing microorganisms, both aerobic and anaerobic will also be included in future studies. The microbial ecology of groundwater has until recently not been investigated, but knowledge of the potential of bacteria from subsurface soil is of increasing interest, owing to pollution of the groundwater system from agricultural cultivation practice and landfills. The Ministry of the Environment has financially supported participation in a large Danish research programme concerning degradation in and leaching from landfills. The ecology of groundwater bacteria has been investigated and further support has been given to a research project concerning degradation of chlorinated aIiphatic compounds by methane-oxidizing bacteria. Investigations to optimize secondary degradation of trichloroethylene and tetrachloroethylene by mixed cultures and isolates of methanotrophic bacteria has been carried out, with the purpose of innovating biological treatment of polluted groundwater.
Conclusion In the research areas referred to above the Department of General Microbiology in Copenhagen is involved directly or indirectly. Microbial ecology in Denmark is wider in its scope and other departments or groups are active in different research areas. Marine and limnic sediments have been studied with great success in the Department of Ecology and Genetics in Aarhus, and in recent years several microelectrodes for detailed studies of microbial processes have been developed. A new research group on rhizosphere studies has been established at the Agricultural University, Section for Microbiology. New detection systems are being developed for study of specific bacterial strains (Pseudomonas spp) and their functional role. All of these research areas are simultaneously being studied all over the world and often in cooperation between different research groups. Some of the important global themes are connected with: the microbial response to climate change; the production of toxins in food for man and animals; the dispersal, growth and survival of pathogenic organisms in the environment; the microorganisms in pollution control and bioremidiation; and microbiological control with pathogenic organisms. With the introduction of molecular methods in microbial ecology it seems as if a series of ecological themes will be addressed with appropriate methods. The stability of strains and of populations will be examined, the exchange of genetic material, the adaptation to changing environmental conditions will find new microbial ecology and also of interest for the use of microorganisms by society is expected.
World Journal of Microbiology and Biotechnology, Vol 8 Supplernen~ I . 1992
119
A view on microbial ecology A. Kjoller
There are few occasions where a wider look at the development of research directions is needed. It is a challenge, however, to define one's own place in the research spectrum and attempt to predict some of the new topics to be covered in coming years. Microbial ecology is a rather new discipline within microbiology dealing with the physiology and interactions between microorganisms participating in the biogeochemical processes in the ecosystems. The research in microbial ecology at our laboratory in the Department of General Microbiology, University of Copenhagen has been focused on the ecological role of microorganisms during decomposition of organic matter in deciduous forests. The research has been concentrated on three main topics: denitrification, the role of microfungi and bacteria during decomposition of the litter and anaerobic decomposition of organic matter. The denitrification studies have included determination of the number of organisms, isolation and identification, and measurements of nitrogen (N20) output in situ and from manipulated samples in the laboratory. Microfungi (and bacteria) were enumerated and isolated from leaves' during the 6 to 7 months decomposition period, and the isolates were tested to determine their potential enzymatic capability. The physiology and ecology of anaerobic bacteria included studies of the interactions between sulphatereducing, methane-producing and denitrifying bacteria and the importance of variations in different environmental factors. Even though microorganisms, e.g. bacteria and fungi, have been isolated and studied also in in-situ experiments in natural environments, still more knowledge of occurrence, growth and role in decomposition processes and nitrogen turnover in different ecosystems is needed. It is considered important to study these processes in nature and also to extend the study of the physiology and ecology of microorganisms from natural environments to stressed environments under varying pollution conditions or other A. Kjeller is at the Department of General Microbiology, University of Copenhagen, Solvgade 83 H, DK-1307 Copenhagen K, Denmark.
man-made influence. The changes in and the functional role of the microbial populations during decomposition of forest litter have been investigated during recent years. A continuation of these activities could be possible in a proposed IUBS/IUMS programme (Functional microbial diversity in terrestrial ecosystems). In the proposal the effect of air pollution, acid rain and other environmental disturbances would be included. Another future approach is to continue the in-situ measurements of denitrifying activity in different types of beech forests in which soil pH varies from 4.5 to 6.9. An European network is established between researchers with the aim to examine denitriflcation in different forests in Europe. In this way estimates of nitrogen release from the European woodland ecosystems can be calculated. The previous decomposition and nitrogen turnover projects have been supported by the University of Copenhagen. The future collaboration with other European countries will be granted by the EEC. There is increasing interest for measurements of nitrogen gases and methane escaping to the atmosphere and for environments where these gases are produced. A large international programme, IGBP (International GeosphereBiosphere Programme), has been initiated, and one of the proposed core projects is global change and terrestrial ecosystems. Our future research projects on denitrification and terminal anaerobic carbon decomposition will contribute to this international programme. It is hoped to initiate research in new areas, besides continuing the above-mentioned decomposition and process studies. It is considered vital to take advantage of the new methods offered through the developments in molecular biology and adopt methods for determination of biomass and activity and use new principles for identification of microorganisms. A governmental biotechnology programme was initiated 3 years ago and the Department of General Microbiology hosts the leadership of a centre for environmental biotechnology. Most of the following research areas are included in this programme or are proposed to constitute the basis for a continuation of the centre. The new centre is formed as a centre for the study
9 1992 Rapid Communications of Oxford Ltd World Journal of Microbiology and Biolechnology, Vol 8 5upplemen~ I 9 I992
117
A. Kjo]ler of microbial ecology including environmental and molecular microbial ecology projects.
Microbial Differentiation and Growth Rates in Nature Microorganisms, bacteria and fungi are known to survive and even grow under very unfavourable conditions, e.g. very low nutrient concentrations, in the environment. Some bacteria are obligate oligotrophs, inhibited by high nutrient concentrations, in contrast to fungi which probably are always able to grow at both high and low nutrient concentrations. The importance of oligotrophic growth conditions for the activity of microfungi is unknown and will be investigated with isolates from natural environments. The concentration of nutrients has been shown to influence both growth rate and morphology of the colony. The ability of the individual strains in a population to adapt to different and varying environmental conditions also needs more research. Combinations of ecological, genetical and molecular methods could be used. More information on stress-induced genes in laboratory strains and in strains isolated from their natural habitat would be of interest. Growth rates of bacteria and fungi in natural environments have been very difficult to determine using traditional methods. By innovation of extraction methods and determination of specific cell components it would be possible to measure and estimate growth rate and growth state of the cells in situ.
Degradation of Organic Compounds The previous studies of processes and the role of microorganisms in decomposition of natural organic matter will be continued. Furthermore, degradation studies of man-made organic compounds (xenobiotics) will be intensified, including the importance of interactions between populations of microorganisms, and the environmental factors determining the degrading activity. Physiological characterization of the microbial populations or single strains able to decompose certain xenobiotic compounds is important as is determination of the metabolic pathways during aerobic or anaerobic conditions. Analysis of metabolic activities is necessary before trying to optimize a degradation process. Genetic characterization of strains with specific degradation ability is a necessary basis for future genetic manipulation.
Molecular Microbial Ecology Use of methods from molecular microbiology in microbial ecology will be intensified in the future. Genetic
I 18
World Journal of Microbiology and Biotechnology, Vol 8 Supplement I 9 I992
manipulation directed towards development of new strains with specific abilities, use of markers, identification of bacteria with immuno-techniques, development of new probes, investigation of plasmid transfer in the natural environment, are some of the specific topics for future research. Deliberate release of genetically manipulated microorganisms (GEMs) to nature (e.g. soil) is not permitted yet. The effect of a massive release of microorganisms on natural ecosystems is unknown, and before any permission is issued, investigation of establishment and survival in relevant niches of the GEM to be released will be required. A complex of factors determines the establishment and proliferation of GEMs released to nature including temperature, oxygen, redox, pH, salinity conditions, special nutrient requirement, resistance to antibiotics, conversion of complex organic substances, etc. It is also important to assess the role of the introduced microorganisms in functional key processes in the ecosystem (e.g. hydrolysis of lignin and cellulose, oxidation of ammonia, and reduction of nitrate), and how the organisms may influence and change the structure of the original population. Studies of these cgmplex ecological features have been initiated, and will be continued. Another trend in molecular microbial ecology is the evaluation of gene transfers in nature. It is known from studies of antibiotic resistance in bacteria that gene transfer takes place between unrelated microorganisms, and that identical antibiotic resistance can be found in a wide variety of bacteria. The future aim is to investigate the dispersal of genes in natural ecosystems using resistance genes as model for the dispersal without selective advantages for the host. This project has obtained support from The Nordic Council of Ministers included in a larger programme concerning the environmental risk by deliberate release of genetic manipulated microorganisms. Other projects have been initiated at the University of Bergen, Norway; Helsinki, Finland and G6teborg, Sweden. Other research projects in microbial ecology in Denmark include the following main subjects and tendencies. (1) Microscale studies of the microbial nitrogen cycling associated with the organic particle fraction in the soil is emphasized. Innovation and adaption of new techniques are needed for the study of microbial populations and processes in undisturbed soil samples or in the rhizosphere. A variety of methods are already in use but methods employing molecular biology are of interest, and a collaboration between molecular biologists and microbial ecologists has been initiated. (2) Microbial processes in oxic and anoxic gradient environments. Processes and population studies in sediments and biofilm will be investigated using microelectrodes and probe techniques to evaluate the regulation of aerobic and anaerobic decomposition of organic matter and sulphur
Microbial ecology in Denmark compounds, oxidation of methane, and further to determine the occurrence and zonation of the bacterial populations. (3) Microbial interactions and regulation of the microbial activity during strict anaerobic turnover of organic matter and man-made (xenobiotic) compounds. Facilities for anaerobic cultivation of bacteria (and fungi) are available in several laboratories and new results of the physiology of anaerobic organisms will emerge and may be used for bioremediation purposes. The importance of varying environmental factors on decomposition processes and microbial interactions, and determination of the kinetics during decomposition of xenobiotic compounds are some of the subjects to be investigated during the following years. Molecular methods will be applied to detect and identify important groups of anaerobic bacteria. Physiological and genetic characterization of xenobiotic decomposing microorganisms, both aerobic and anaerobic will also be included in future studies. The microbial ecology of groundwater has until recently not been investigated, but knowledge of the potential of bacteria from subsurface soil is of increasing interest, owing to pollution of the groundwater system from agricultural cultivation practice and landfills. The Ministry of the Environment has financially supported participation in a large Danish research programme concerning degradation in and leaching from landfills. The ecology of groundwater bacteria has been investigated and further support has been given to a research project concerning degradation of chlorinated aIiphatic compounds by methane-oxidizing bacteria. Investigations to optimize secondary degradation of trichloroethylene and tetrachloroethylene by mixed cultures and isolates of methanotrophic bacteria has been carried out, with the purpose of innovating biological treatment of polluted groundwater.
Conclusion In the research areas referred to above the Department of General Microbiology in Copenhagen is involved directly or indirectly. Microbial ecology in Denmark is wider in its scope and other departments or groups are active in different research areas. Marine and limnic sediments have been studied with great success in the Department of Ecology and Genetics in Aarhus, and in recent years several microelectrodes for detailed studies of microbial processes have been developed. A new research group on rhizosphere studies has been established at the Agricultural University, Section for Microbiology. New detection systems are being developed for study of specific bacterial strains (Pseudomonas spp) and their functional role. All of these research areas are simultaneously being studied all over the world and often in cooperation between different research groups. Some of the important global themes are connected with: the microbial response to climate change; the production of toxins in food for man and animals; the dispersal, growth and survival of pathogenic organisms in the environment; the microorganisms in pollution control and bioremidiation; and microbiological control with pathogenic organisms. With the introduction of molecular methods in microbial ecology it seems as if a series of ecological themes will be addressed with appropriate methods. The stability of strains and of populations will be examined, the exchange of genetic material, the adaptation to changing environmental conditions will find new microbial ecology and also of interest for the use of microorganisms by society is expected.
World Journal of Microbiology and Biotechnology, Vol 8 Supplernen~ I . 1992
119
