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INTRODUCTION Soils constitute a primordial compartment of terrestrial ecosystems. They are the interface between earth mineral layer and the biosphere. They result both from the degradation of the mineral parent rock releasing essential nutrients for life, and the accumulation of dead organic matter. Nutrients sequestrated in dead organic matter are recycled by soil microbes, which is an essential condition for the maintenance of primary production. Moreover, huge quantities of carbon are sequestered in the recalcitrant part of soil organic matter over centuries to millennia [1,2] before being released as CO2. On the long term, this sequestration influences the quantity of atmospheric CO2 and the climate [3]. Hence, soils play a fundamental role in all biogeochemical cycles. Soil processes depend on physical and chemical parameters (climate, parent rock) but also depend on many soil organisms such as bacteria, fungus, mesofauna (collembola, mite), macrofauna (earthworm, termite, ant, insect larvae, millipede…) and plants. The study of the interactions between these organisms, and between these organisms and their physical environment has required the development of a whole scientific domain: soil ecology. Besides the desire to increase ecological knowledge, the importance of the involved applied issues (soil fertility, soils as a carbon sink…etc) has strongly fostered the development of soil ecology as proved by the existence of many specialized journals. The field is currently making wide progresses. For example, many recent studies reveal new mechanisms that could deeply influence soil fertility, competition between plants or ecosystem reaction to global change [4–6]. However, the feeling has developed among some soil scientists that soil ecology has developed too independently from the rest of ecology and that soil ecology is short of modelling and evolutionary approaches [7–9]. Hence soil ecology seems to have had a small influence on the development of contemporary ecology and, conversely, many useful ecological concepts have not been used to interpret soil processes. To test quantitatively the veracity of these hypotheses and to analyse better the place of soil ecology within ecology we have achieved a wide bibliographic analysis. We aimed at providing the evidence that soil ecologists make a parsimonious use of modelling and evolutionary interpretations: (1) soil ecology journals publish low percentages of articles based on a modelling or evolutionary approaches, (2) journals specialized in evolution and modelling publish low percentages of articles related to soil ecology and (3) there are low percentages of cross-citations between soil ecology journals and journals specialized in modelling and evolutionary approaches. We also aimed at showing that the links between soil ecology and general ecology are sparse: (4) there are low percentages of soil ecology articles published in generalist ecology journals and (5) there are low percentages of cross-citations between generalist ecology journals and soil ecology journals. We thus tested five hypotheses. In the discussion we analysed the results of these five tests and try to give proximal and historical explanations to the position of soil ecology within ecology. We finally conclude with some remarks on the way the publication system may have influenced the development of soil ecology. METHODS To assess the position of soil ecology within general ecology and to evaluate the use of modelling and evolutionary approaches we have analysed eight journals specialized in soil ecology (Applied Soil Ecology, Biology and Fertility of Soils, European Journal of Soil Biology, Pedobiologia, Soil Biology and Biochemistry, Plant and Soil), seven generalist journals of ecology (American Naturalist, Ecology, Ecology Letters, J. Animal Ecology, J. Ecology, Functional Ecology, Oikos), two journals specialized in evolution (Evolution and Evolutionary Ecology), and three journals specialized in modelling (Ecological Modelling, Theoretical Population Biology, Journal of Theoretical Biology). J. Animal Ecology, J. Ecology and Functional Ecology are arguably less general than the other generalist journals but taken together they are the equivalent of Ecology for the British Ecological Society. This list is not comprehensive but was designed to allow comparing clear-cut cases, i.e. journals publishing respectively only articles related to soil ecology, evolution and modelling and journals publishing articles related to all fields of ecology. The data base, ISI Web of Knowledge, was scanned from 1997 to 2004 (from 1998 for Ecology Letters). Overall, this represents about 23000 papers for the considered journals. To find all articles dealing with soil ecology in journals not specialized in soil ecology the word ‘‘soil’’ was searched for in titles, key-words and abstracts. Conversely, it was searched for the words ‘‘evolution’’ and ‘‘model’’ in journals not specialized in evolution or modelling. All abstracts were looked through to eliminate irrelevant articles. We checked beforehand that searching for these general terms allows gathering most relevant papers but that the ‘‘manual’’ sorting was necessary due to the poor selectivity of these terms. It is difficult to give a precise definition of soil ecology. However, we considered as linked to soil ecology any study dealing with soil organisms, parts of organisms dwelling in soils (root), soil processes involving organisms (mineralization, soil respiration) or processes linking soil and aboveground organisms. For the selection of papers dealing with models, studies only using statistical models or null models were rejected as well as studies only mentioning a published model to state that their empirical results support or not the conclusions of these models. For the selection of papers dealing with evolution, studies addressing directly an evolutionary issue or only interpreting empirical data using evolutionary theories were taken into account. We first calculated, for each journal, the percentage of articles dealing with soil ecology, modelling and evolution. We then assessed the relations between the percentage of articles dealing with soil ecology and respectively the Impact Factor of the journals, the percentage of articles based on modelling and the percentage of articles based on an evolutionary approach. This allowed comparing journals and types of journals (specialized in soil ecology vs. generalist or specialized in evolution or modelling) but this did not allow comparing articles published in different fields of ecology (for example bird ecology vs. soil ecology). To approach the latter we have also calculated, inside the publications of each of our sample of twelve journals that are non-specialized in soil ecology, the percentage of articles dealing with soil ecology that also use models or also involve evolutionary interpretations. Then, these percentages were compared (x2 test) to the percentages of publications, inside the same non-specialized journals, using models or evolutionary interpretations but not dealing with soil ecology, i.e. publications related to all other fields of ecology such as bird ecology. The development of a scientific field should also be reflected in the publications of very generalist and highly cited journals such as Science and Nature. We searched for the articles dealing with soils published in these journals between 1997 and 2004 (searching for the word soil in the title, abstract and key-words and eliminating manually non relevant articles) and classified coarsely the content of these articles. So far, the analyses aimed at assessing the position of soil ecology within general ecology by counts of articles dealing with soil ecology in different categories of journals. Citations might also constitute important links between scientific fields and more specifically between soil ecology and general ecology/theory/ evolutionary thinking. We have thus examined the articles cited by the articles of three issues of Soil Biology and Biochemistry (2003, volume 35, issues 10, 11, 12) and the articles citing these articles published in SBB. These articles were classified in broad categories: Model, Generalist journals, Animal, Plant, Ecology, Agronomy, Soil sciences, Microbiology, Miscellaneous, Soil Ecology. ‘‘Model’’ refers to the journal specialized in modelling (the one cited above in the first paragraphs of the section). ‘‘Generalist journals’’ are journals such as Science, Nature and Proceedings of the Royal Society London. ‘‘Animal’’ and ‘‘Plant’’ refer to journals studying animals and plant but not specifically their ecology (for example Nematology and Plant Physiology). ‘‘Ecology’’ and ‘‘Soil ecology’’ refers to generalist ecology journals and journals specialized in soil ecology such as the once cited above in the first paragraph of the section. ‘‘Agronomy’’ refers to journals specialized in the application of soil and ecological sciences for plant production. ‘‘Soil sciences’’ refer to journals about soils but with little emphasis on biological and ecological processes such as the European Journal of Soil Sciences. ‘‘Microbiology’’ refers to microbiology journals. ‘‘Miscellaneous’’ refers to journals difficult to classify, mostly journals about specific scientific tools such as Rapid Communications in Mass Spectrometry or journals about specific type of environment such as Canadian Journal of Forest Research. RESULTS As expected, Journals specialized in soil ecology have lower impact factors (IF) than generalist journals (Table 1, see also Fig. 1 the loglog significant relation between IF and percentages of papers dealing with soil ecology). More interestingly, a low percentage of the papers published in the generalist journals deals with soil ecology; less than 6 % in most cases but 20% for Journal of Ecology and 13.8% for Oikos. At the same time, generalist journals publish much more studies using modelling (between 11.4 and 36.2%) than soil ecology journals do (between 0.4 and 6.3 %, see Table 1). It must be marked that the two generalist journals publishing the less modelbased studies are the ones publishing the more soil-related papers (Functional Ecology and Journal of Ecology). Conversely, ecology journals specialized in modelling (Theoretical Population Biology and Journal of Theoretical Biology) publish few papers about soil ecology (respectively 0.8 and 1.3 %). Ecological Modelling which is less theoretically oriented publishes a higher percentage of papers dealings with soil (10.7 %). There is a significant negative correlation between the proportion of papers dealing with soil ecology and the proportion of papers based on models (Fig. 1). In the same vein, generalist papers publish much more studies dealing with evolution (between 10.6 and 45.6 % in most cases, 10.6 for Oikos, but 3.9 % for Journal of Ecology) than journals specialized in soil ecology (between 0.1 and 1 %, see Table 1). Again, the generalist journal publishing the highest percentage of soil ecology-related articles, Journal of Ecology, also publishes the fewest studies dealing with evolution. Overall there is a significant negative relationship between the percentage of articles dealing with soil ecology and the percentage of articles tackling evolutionary issues (Fig. 1). We also tested whether evolutionary journals publish high percentages of studies using modelling and conversely that theoretical-oriented journals publish high percentages of studies dealing with evolution. These hypotheses hold for all journals but for Ecological Modelling whose papers rarely deal with evolution (Tab. 1). This journal publishes more papers about soil ecology than Journal of Theoretical Biology and Theoretical Population biology. This suggests the existence of a link between evolutionary thinking and ecological modelling and confirms the independence of soil ecology from this evolutionary-modelling pole. In most cases, in journals non-specialized in soil ecology, the percentage of articles using a model or an evolutionary interpretation is lower for soil ecology articles than for the other articles and most of these differences were significant (Table 1, x2 tests). The exceptions mainly correspond to journals publishing low numbers of articles dealing with soil ecology (American Naturalist, Evolutionary Ecology, J. Animal Ecology). In these cases, very few articles (fewer than 10) are concerned so that the validity and significance of x2 tests are dubious. Overall, when journals non-specialised in soil ecology or theory are pooled, respectively 11.4 % and 20.2 % of soil ecology articles and non-soil ecology articles use modelling. This difference is highly significant (x2 test, df = 1, P,0.001). Similarly, in journals non-specialised in soil ecology or evolution, respectively 7.3 % and 29.4 % of soil ecology articles and non-soil ecology articles use evolutionary interpretations. This difference is also highly significant (x2 test, df= 1, P,0.001). These results suggest that soil ecologists use more parsimoniously modelling and evolutionary approaches than ecologists of other fields. Science and Nature publish both about 0.4 % of papers having a connection with soils. Among these articles, about 40 % (41.96 % for Nature, 45.56 % for Science) of the published studies deal with purely physical issues such as transport of particles at a global scale, and with mars and lunar soils. It remains about 60 % of terrestrial soil-related articles (about 0.25 % of all published articles) that can be considered as dealing with soil ecology (see above explanations on the type of studies considered as soil ecology). For Nature and Science, respectively, 50 % and 25 % of these studies related to soil ecology deal with global change issues. Typically, the response of a soil parameter or a soil community to an increase in the atmospheric CO2 level or temperature is examined [10,11]. Such studies are of course important in the present context. However, many of them tend not to analyse directly the specific and poorly known mechanisms linking soil microflora, soil macroorganims, plants and soil processes [but see12,13]. Figure 2 displays the distribution of articles cited by and citing the articles of the three sampled issues of SBB. 43 articles have been published in these issues. They cite about 1400 other articles and have so far been cited by about 300 articles. These articles (citing SBB and cited by SBB) have nearly the same structure according to our classification. About 6 % of these articles belongs to the category ‘‘General ecology’’. No journal specialized in evolutionary ecology cites SBB or is cited by SBB. None of the articles cited by SBB and only two articles citing SBB have been published in journals specialized in modelling. The majority of articles cited by or citing SBB have been published in soil ecology journals (about 30%). About 18 and 12% of these articles have been published in microbiology journals. About 10 % of these articles cited have been published in journals specialized respectively in soil sciences or agronomy.
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번역 잘하시는 분은 좀 도와주세요. 너무 궁금합니다~!
6월 18일 까지 부탁드릴께요~!
INTRODUCTION Soils constitute a primordial compartment of terrestrial ecosystems. They are the interface between earth mineral layer and the biosphere. They result both from the degradation of the mineral parent rock releasing essential nutrients for life, and the accumulation of dead organic matter. Nutrients sequestrated in dead organic matter are recycled by soil microbes, which is an essential condition for the maintenance of primary production. Moreover, huge quantities of carbon are sequestered in the recalcitrant part of soil organic matter over centuries to millennia [1,2] before being released as CO2. On the long term, this sequestration influences the quantity of atmospheric CO2 and the climate [3]. Hence, soils play a fundamental role in all biogeochemical cycles. Soil processes depend on physical and chemical parameters (climate, parent rock) but also depend on many soil organisms such as bacteria, fungus, mesofauna (collembola, mite), macrofauna (earthworm, termite, ant, insect larvae, millipede…) and plants. The study of the interactions between these organisms, and between these organisms and their physical environment has required the development of a whole scientific domain: soil ecology. Besides the desire to increase ecological knowledge, the importance of the involved applied issues (soil fertility, soils as a carbon sink…etc) has strongly fostered the development of soil ecology as proved by the existence of many specialized journals. The field is currently making wide progresses. For example, many recent studies reveal new mechanisms that could deeply influence soil fertility, competition between plants or ecosystem reaction to global change [4–6]. However, the feeling has developed among some soil scientists that soil ecology has developed too independently from the rest of ecology and that soil ecology is short of modelling and evolutionary approaches [7–9]. Hence soil ecology seems to have had a small influence on the development of contemporary ecology and, conversely, many useful ecological concepts have not been used to interpret soil processes. To test quantitatively the veracity of these hypotheses and to analyse better the place of soil ecology within ecology we have achieved a wide bibliographic analysis. We aimed at providing the evidence that soil ecologists make a parsimonious use of modelling and evolutionary interpretations: (1) soil ecology journals publish low percentages of articles based on a modelling or evolutionary approaches, (2) journals specialized in evolution and modelling publish low percentages of articles related to soil ecology and (3) there are low percentages of cross-citations between soil ecology journals and journals specialized in modelling and evolutionary approaches. We also aimed at showing that the links between soil ecology and general ecology are sparse: (4) there are low percentages of soil ecology articles published in generalist ecology journals and (5) there are low percentages of cross-citations between generalist ecology journals and soil ecology journals. We thus tested five hypotheses. In the discussion we analysed the results of these five tests and try to give proximal and historical explanations to the position of soil ecology within ecology. We finally conclude with some remarks on the way the publication system may have influenced the development of soil ecology. METHODS To assess the position of soil ecology within general ecology and to evaluate the use of modelling and evolutionary approaches we have analysed eight journals specialized in soil ecology (Applied Soil Ecology, Biology and Fertility of Soils, European Journal of Soil Biology, Pedobiologia, Soil Biology and Biochemistry, Plant and Soil), seven generalist journals of ecology (American Naturalist, Ecology, Ecology Letters, J. Animal Ecology, J. Ecology, Functional Ecology, Oikos), two journals specialized in evolution (Evolution and Evolutionary Ecology), and three journals specialized in modelling (Ecological Modelling, Theoretical Population Biology, Journal of Theoretical Biology). J. Animal Ecology, J. Ecology and Functional Ecology are arguably less general than the other generalist journals but taken together they are the equivalent of Ecology for the British Ecological Society. This list is not comprehensive but was designed to allow comparing clear-cut cases, i.e. journals publishing respectively only articles related to soil ecology, evolution and modelling and journals publishing articles related to all fields of ecology. The data base, ISI Web of Knowledge, was scanned from 1997 to 2004 (from 1998 for Ecology Letters). Overall, this represents about 23000 papers for the considered journals. To find all articles dealing with soil ecology in journals not specialized in soil ecology the word ‘‘soil’’ was searched for in titles, key-words and abstracts. Conversely, it was searched for the words ‘‘evolution’’ and ‘‘model’’ in journals not specialized in evolution or modelling. All abstracts were looked through to eliminate irrelevant articles. We checked beforehand that searching for these general terms allows gathering most relevant papers but that the ‘‘manual’’ sorting was necessary due to the poor selectivity of these terms. It is difficult to give a precise definition of soil ecology. However, we considered as linked to soil ecology any study dealing with soil organisms, parts of organisms dwelling in soils (root), soil processes involving organisms (mineralization, soil respiration) or processes linking soil and aboveground organisms. For the selection of papers dealing with models, studies only using statistical models or null models were rejected as well as studies only mentioning a published model to state that their empirical results support or not the conclusions of these models. For the selection of papers dealing with evolution, studies addressing directly an evolutionary issue or only interpreting empirical data using evolutionary theories were taken into account. We first calculated, for each journal, the percentage of articles dealing with soil ecology, modelling and evolution. We then assessed the relations between the percentage of articles dealing with soil ecology and respectively the Impact Factor of the journals, the percentage of articles based on modelling and the percentage of articles based on an evolutionary approach. This allowed comparing journals and types of journals (specialized in soil ecology vs. generalist or specialized in evolution or modelling) but this did not allow comparing articles published in different fields of ecology (for example bird ecology vs. soil ecology). To approach the latter we have also calculated, inside the publications of each of our sample of twelve journals that are non-specialized in soil ecology, the percentage of articles dealing with soil ecology that also use models or also involve evolutionary interpretations. Then, these percentages were compared (x2 test) to the percentages of publications, inside the same non-specialized journals, using models or evolutionary interpretations but not dealing with soil ecology, i.e. publications related to all other fields of ecology such as bird ecology. The development of a scientific field should also be reflected in the publications of very generalist and highly cited journals such as Science and Nature. We searched for the articles dealing with soils published in these journals between 1997 and 2004 (searching for the word soil in the title, abstract and key-words and eliminating manually non relevant articles) and classified coarsely the content of these articles. So far, the analyses aimed at assessing the position of soil ecology within general ecology by counts of articles dealing with soil ecology in different categories of journals. Citations might also constitute important links between scientific fields and more specifically between soil ecology and general ecology/theory/ evolutionary thinking. We have thus examined the articles cited by the articles of three issues of Soil Biology and Biochemistry (2003, volume 35, issues 10, 11, 12) and the articles citing these articles published in SBB. These articles were classified in broad categories: Model, Generalist journals, Animal, Plant, Ecology, Agronomy, Soil sciences, Microbiology, Miscellaneous, Soil Ecology. ‘‘Model’’ refers to the journal specialized in modelling (the one cited above in the first paragraphs of the section). ‘‘Generalist journals’’ are journals such as Science, Nature and Proceedings of the Royal Society London. ‘‘Animal’’ and ‘‘Plant’’ refer to journals studying animals and plant but not specifically their ecology (for example Nematology and Plant Physiology). ‘‘Ecology’’ and ‘‘Soil ecology’’ refers to generalist ecology journals and journals specialized in soil ecology such as the once cited above in the first paragraph of the section. ‘‘Agronomy’’ refers to journals specialized in the application of soil and ecological sciences for plant production. ‘‘Soil sciences’’ refer to journals about soils but with little emphasis on biological and ecological processes such as the European Journal of Soil Sciences. ‘‘Microbiology’’ refers to microbiology journals. ‘‘Miscellaneous’’ refers to journals difficult to classify, mostly journals about specific scientific tools such as Rapid Communications in Mass Spectrometry or journals about specific type of environment such as Canadian Journal of Forest Research. RESULTS As expected, Journals specialized in soil ecology have lower impact factors (IF) than generalist journals (Table 1, see also Fig. 1 the loglog significant relation between IF and percentages of papers dealing with soil ecology). More interestingly, a low percentage of the papers published in the generalist journals deals with soil ecology; less than 6 % in most cases but 20% for Journal of Ecology and 13.8% for Oikos. At the same time, generalist journals publish much more studies using modelling (between 11.4 and 36.2%) than soil ecology journals do (between 0.4 and 6.3 %, see Table 1). It must be marked that the two generalist journals publishing the less modelbased studies are the ones publishing the more soil-related papers (Functional Ecology and Journal of Ecology). Conversely, ecology journals specialized in modelling (Theoretical Population Biology and Journal of Theoretical Biology) publish few papers about soil ecology (respectively 0.8 and 1.3 %). Ecological Modelling which is less theoretically oriented publishes a higher percentage of papers dealings with soil (10.7 %). There is a significant negative correlation between the proportion of papers dealing with soil ecology and the proportion of papers based on models (Fig. 1). In the same vein, generalist papers publish much more studies dealing with evolution (between 10.6 and 45.6 % in most cases, 10.6 for Oikos, but 3.9 % for Journal of Ecology) than journals specialized in soil ecology (between 0.1 and 1 %, see Table 1). Again, the generalist journal publishing the highest percentage of soil ecology-related articles, Journal of Ecology, also publishes the fewest studies dealing with evolution. Overall there is a significant negative relationship between the percentage of articles dealing with soil ecology and the percentage of articles tackling evolutionary issues (Fig. 1). We also tested whether evolutionary journals publish high percentages of studies using modelling and conversely that theoretical-oriented journals publish high percentages of studies dealing with evolution. These hypotheses hold for all journals but for Ecological Modelling whose papers rarely deal with evolution (Tab. 1). This journal publishes more papers about soil ecology than Journal of Theoretical Biology and Theoretical Population biology. This suggests the existence of a link between evolutionary thinking and ecological modelling and confirms the independence of soil ecology from this evolutionary-modelling pole. In most cases, in journals non-specialized in soil ecology, the percentage of articles using a model or an evolutionary interpretation is lower for soil ecology articles than for the other articles and most of these differences were significant (Table 1, x2 tests). The exceptions mainly correspond to journals publishing low numbers of articles dealing with soil ecology (American Naturalist, Evolutionary Ecology, J. Animal Ecology). In these cases, very few articles (fewer than 10) are concerned so that the validity and significance of x2 tests are dubious. Overall, when journals non-specialised in soil ecology or theory are pooled, respectively 11.4 % and 20.2 % of soil ecology articles and non-soil ecology articles use modelling. This difference is highly significant (x2 test, df = 1, P,0.001). Similarly, in journals non-specialised in soil ecology or evolution, respectively 7.3 % and 29.4 % of soil ecology articles and non-soil ecology articles use evolutionary interpretations. This difference is also highly significant (x2 test, df= 1, P,0.001). These results suggest that soil ecologists use more parsimoniously modelling and evolutionary approaches than ecologists of other fields. Science and Nature publish both about 0.4 % of papers having a connection with soils. Among these articles, about 40 % (41.96 % for Nature, 45.56 % for Science) of the published studies deal with purely physical issues such as transport of particles at a global scale, and with mars and lunar soils. It remains about 60 % of terrestrial soil-related articles (about 0.25 % of all published articles) that can be considered as dealing with soil ecology (see above explanations on the type of studies considered as soil ecology). For Nature and Science, respectively, 50 % and 25 % of these studies related to soil ecology deal with global change issues. Typically, the response of a soil parameter or a soil community to an increase in the atmospheric CO2 level or temperature is examined [10,11]. Such studies are of course important in the present context. However, many of them tend not to analyse directly the specific and poorly known mechanisms linking soil microflora, soil macroorganims, plants and soil processes [but see12,13]. Figure 2 displays the distribution of articles cited by and citing the articles of the three sampled issues of SBB. 43 articles have been published in these issues. They cite about 1400 other articles and have so far been cited by about 300 articles. These articles (citing SBB and cited by SBB) have nearly the same structure according to our classification. About 6 % of these articles belongs to the category ‘‘General ecology’’. No journal specialized in evolutionary ecology cites SBB or is cited by SBB. None of the articles cited by SBB and only two articles citing SBB have been published in journals specialized in modelling. The majority of articles cited by or citing SBB have been published in soil ecology journals (about 30%). About 18 and 12% of these articles have been published in microbiology journals. About 10 % of these articles cited have been published in journals specialized respectively in soil sciences or agronomy.
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