Applied and Environmental Microbiology, Mar 1, 2003
The potential for oxidation of ammonia in anoxic marine sediments exists through anaerobic oxidat... more The potential for oxidation of ammonia in anoxic marine sediments exists through anaerobic oxidation by Nitrosomonas-like organisms, utilizing nitrogen dioxide, coupling of nitrification, manganese reduction, and anaerobic oxidation of ammonium by planctomycetes (the Anammox process). Here we describe the presence of microbial communities with the potential to carry out these processes in a natural marine sediment system (Loch Duich, Scotland). Natural microbial communities of Planctomycetales-Verrucomicrobia and -and ␥-proteobacterial ammonia-oxidizing bacteria were characterized by analysis of 16S rRNA genes amplified using group-specific primers by PCR-and reverse transcription-PCR amplification of 16S rDNA and RNA, respectively. Amplification products were analyzed by sequencing of clones and by denaturant gradient gel electrophoresis (DGGE). Amplification of primers specific for Planctomycetales-Verrucomicrobia and -proteobacterial ammonia-oxidizing bacteria generated products at all sampling sites and depths, but no product was generated using primers specific for ␥-proteobacterial ammonia-oxidizing bacteria. 16S rDNA DGGE banding patterns indicated complex communities of -proteobacterial ammonia-oxidizing bacteria in anoxic marine sediments. Phylogenetic analysis of sequences from clones and those excised from DGGE gels suggests dominance of Nitrosospira cluster 1-like organisms and of strains belonging to a novel cluster represented in dominant bands in 16S rRNA DGGE banding patterns. Their presence indicates a group of organisms closely related to recognized -proteobacterial ammonia-oxidizing bacteria that may be selected in anoxic environments and may be capable of anoxic ammonia oxidation. Sequence analysis of planctomycete clone libraries and sequences excised from DGGE gels also demonstrated a diverse microbial community and suggested the presence of new subdivisions, but no sequence related to recognized Anammox organisms was detected.
The environment disseminates antimicrobial-resistance genes; however, it remains challenging to d... more The environment disseminates antimicrobial-resistance genes; however, it remains challenging to distinguish whether human activities exacerbate antimicrobial resistance or what is natural. Here, we quantified ~300 resistance-related genes in 200+ Scottish soil samples. Location or land use does not explain gene differences, but nutrient levels reduce gene richness. Elevated levels of metals increased gene richness, and selenium increased transposase levels. Rainfall and persistent organic pollutants also increased transposase relative abundance, possibly promoting conditions conducive to the horizontal transfer of antimicrobial-resistance genes. Selenium and polychlorinated biphenyls were primary factors in gene abundance, while polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pH influenced gene diversity. Polychlorinated biphenyls are derived from anthropogenic activities, highlighting human activities’ potential impact on gene prevalence. This is the first national...
One of the main drivers for the recent interest in utilising fungi has been the development of mo... more One of the main drivers for the recent interest in utilising fungi has been the development of molecular technologies which allow us to investigate fungal communities in detail. We have made significant steps forward in understanding numbers and functions of fungal communities in soil. If we are to make progress in harnessing fungal communities for improving the sustainability of our production systems, we need to improve our ability to accurately monitor species composition, abundance and interactions, and to increase our understanding of functional traits. This chapter presents recent advances in the study of these ubiquitous and vital components of all terrestrial ecosystems.
Ammonia oxidation, as the first step in the nitrification process, plays a central role in the gl... more Ammonia oxidation, as the first step in the nitrification process, plays a central role in the global cycling of nitrogen. Although bacteria are traditionally considered to be responsible for ammonia oxidation, a role for archaea has been suggested by data from metagenomic studies and by the isolation of a marine, autotrophic, ammonia-oxidizing, non-thermophilic crenarchaeon. Evidence for ammonia oxidation by non-thermophilic crenarchaea in marine and terrestrial environments is largely based on abundance of bacterial and archaeal ammonia monooxygenase (amo) genes, rather than activity. In this study, we have determined the influence of temperature on the response of ammonia-oxidizing bacteria and archaea in nitrifying soil microcosms using two approaches, involving analysis of transcriptional activity of 16S rRNA genes and of a key functional gene, amoA, which encodes ammonia monooxygenase subunit A. There was little evidence of changes in relative abundance or transcriptional activity of ammoniaoxidizing bacteria during nitrification. In contrast, denaturing gradient gel electrophoresis analysis of crenarchaeal 16S rRNA and crenarchaeal amoA genes provided strong evidence of changes in community structure of active archaeal ammonia oxidizers. Community structure changes were similar during incubation at different temperatures and much of the activity was due to a group of non-thermophilic crenarchaea associated with subsurface and marine environments, rather than soil. The findings suggest a role for crenarchaea in soil nitrification and that further information is required on their biogeography.
The relationship between biogeochemical process rates and microbial functional activity was inves... more The relationship between biogeochemical process rates and microbial functional activity was investigated by analysis of the transcriptional dynamics of the key functional genes for methanogenesis (methyl coenzyme M reductase; mcrA) and methane oxidation (particulate methane monooxygenase; pmoA) and in situ methane flux at two peat soil field sites with contrasting net methane-emitting and -oxidizing characteristics. qPCR was used to quantify the abundances of mcrA and pmoA genes and transcripts at two soil depths. Total methanogen and methanotroph transcriptional dynamics, calculated from mcrA and pmoA gene : transcript abundance ratios, were similar at both sites and depths. However, a linear relationship was demonstrated between surface mcrA and pmoA transcript dynamics and surface flux rates at the methane-emitting and methane-oxidizing sites, respectively. Results indicate that methanotroph activity was at least partially substrate-limited at the methane-emitting site and by oth...
Pasteuria spp. are endospore forming bacteria which act as natural antagonists to many of the mos... more Pasteuria spp. are endospore forming bacteria which act as natural antagonists to many of the most economically significant plant parasitic nematodes (PPNs). Highly speciesspecific nematode suppression may be observed in soils containing a sufficiently high density of Pasteuria spp. spores. This suppression is enacted by the bacteria via inhibition of root invasion and sterilization of the nematode host. Molecular methods for the detection of Pasteuria spp. from environmental DNA (eDNA) have been described; however, these methods are limited in both scale and in depth. We report the use of small subunit rRNA gene metabarcoding to profile Pasteuria spp. and nematode communities in parallel. We have investigated Pasteuria spp. population structure in Scottish soils using eDNA from two sources: soil extracted DNA from the second National Soil Inventory of Scotland (NSIS2); and nematode extracted DNA collected from farms in the East Scotland Farm Network (ESFN). We compared the Pasteuria spp. community culture to both nematode community structure and the physiochemical properties of soils. Our results indicate that Pasteuria spp. populations in Scottish soils are broadly dominated by two sequence variants. The first of these aligns with high identity to Pasteuria hartismeri, a species first described parasitizing Meloidogyne ardenensis, a nematode parasite of woody and perennial plants in northern Europe. The second aligns with a Pasteuria-like sequence which was first recovered from a farm near Edinburgh which was found to contain bacterial feeding nematodes and Pratylenchus spp. encumbered by Pasteuria spp. endospores. Further, soil carbon, moisture, bulk density, and pH showed a strong correlation with the Pasteuria spp. community composition. These results indicate that metabarcoding is appropriate for the sensitive, specific, and semi-quantitative profiling of Pasteuria species from eDNA.
Streams and rivers are an important source of CO 2 emissions 1. One important control of these em... more Streams and rivers are an important source of CO 2 emissions 1. One important control of these emissions is the metabolic balance between photosynthesis, which converts CO 2 to organic carbon, and respiration, which converts organic carbon into CO 2 (refs 2,3). Carbon emissions from rivers could increase with warming, independently of organic carbon inputs, because the apparent activation energy is predicted to be higher for respiration than photosynthesis 4,5. However, physiological CO 2-concentrating mechanisms may prevent the increase in photorespiration, limiting photosynthesis with warming 6. Here we report the thermal response of aquatic photosynthesis from streams located in geothermal areas of North America, Iceland and Kamchatka with water temperatures ranging between 4 and 70 • C. Based on a thermodynamic theory of enzyme kinetics, we show that the apparent activation energy of aquatic ecosystem photosynthesis is approximately 0.57 electron volts (eV) for temperatures ranging from 4 to 45 • C, which is similar to that of respiration 4,5,7-9. This result and a global synthesis of 222 streams suggest that warming will not create increased stream and river CO 2 emissions from a warming-induced imbalance between photosynthesis and respiration. However, temperature could a ect annual CO 2 emissions from streams if ecosystem respiration is independent of gross primary production, and may be amplified by increasing organic carbon supply. A key, rate-limiting step during photosynthesis is CO 2-fixing by the D-ribulose-1,5-bisphosphate carboxylase/oxygenase enzyme (Rubisco) 10,11. The average activation energy of Rubisco carboxylase activity across phylogenetic groups is about 0.57 eV (chlorophytes 0.30 eV, cyanobacteria 0.44 eV, spermatophytes 0.63 eV, diatoms 0.65 eV, rhodophytes 0.82 eV) (refs 12,13) and is similar to the respiratory complex, but it becomes less efficient with warming under the decreasing solubility of CO 2 /O 2 concentration ratio in solution leading to photorespiration (fixation of O 2 instead of CO 2) (refs 10,11,14). This creates a difference in apparent (or effective) activation energies between photosynthesis (E a ≈ 0.32 eV, based on C3 terrestrial plant metabolism) 10 and community respiration (E cr ≈ 0.47 to 0.65 eV) (refs 4,5,7-9) predicted to alter the metabolic balance of aquatic ecosystems in response to warming 4,5,15. However, most autotrophic aquatic organisms, contributing to half of the global oxygenic photosynthesis 16 , have evolved a diversity
This study provided an assessment of the environmental fate of antibiotic resistance genes (ARGs)... more This study provided an assessment of the environmental fate of antibiotic resistance genes (ARGs) in a Scottish grassland field repeatedly treated with different organic fertilizers. The impacts of manure, biosolids and municipal food-derived compost on the relative abundances of tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), sulfonamide ARGs (sul1 and sul2) and class 1 integron-integrase gene (IntI1) in soils were investigated, with inorganic fertilizer (NPK) as a comparison. The background soil with a history of low intensity farming showed a higher total relative abundance of tet ARGs over sul ARGs, with tetracycline efflux genes occurring in a higher frequency. In all treatments, the relative abundances of most ARGs detected in soils decreased over time, especially IntI1 and tet ARGs. This general attenuation of soil ARGs is a reflection of changes in the soil microbial community, which is supported by the result that almost all the soils at the end of the experiment had different bacterial communities from the untreated soil at the beginning of the experiment. Multiple applications of organic fertilizers to some extent counteracted the decreasing trend of soil ARGs relative abundances, which resulted in higher ARGs relative abundances in comparison to NPK, either by a lesser decrease of IntI1 and tet ARGs or an increase of sul ARGs. The enhancement of existing soil ARG prevalence by organic fertilizers was strongly dependent on the organic fertilizer type and the particular ARG. Compost contained the lowest relative abundance of inherent ARGs and had the least effect on the soil ARG decrease after application. The relative increase of tet ARGs caused by biosolids was larger than that of sul ARGs, while manure caused the opposite effect. Fertilization practices did not exert effective impacts on the soil bacterial community, although it caused significant changes in the profile of the ARG pool. Organic fertilization may thus accelerate the dissemination of ARGs in soil mainly through horizontal gene transfer (HGT), consistent with the enrichment of IntI1 in organic fertilized soils.
It is well established that resource quantity and elemental stoichiometry play major roles in sha... more It is well established that resource quantity and elemental stoichiometry play major roles in shaping below and aboveground plant biodiversity, but their importance for shaping microbial diversity in soil remains unclear. Here, we used statistical modeling on a regional database covering 179 locations and six ecosystem types across Scotland to evaluate the roles of total carbon (C), nitrogen (N) and phosphorus (P) availabilities and ratios, together with land use, climate and biotic and abiotic factors, in determining regional scale patterns of soil bacterial diversity. We found that bacterial diversity and composition were primarily driven by variation in soil resource stoichiometry (total C:N:P ratios), itself linked to different land uses, and secondarily driven by other important biodiversity drivers such as climate, soil spatial heterogeneity, soil pH, root influence (plant-soil microbe interactions) and microbial biomass (soil microbe-microbe interactions). In aggregate, these...
Rising global temperatures may increase the rates of soil organic matter decomposition by heterot... more Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO 2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor PLOS ONE |
Environmental pollution (Barking, Essex : 1987), Jan 4, 2016
Antibiotics entering the soil likely disturb the complex regulatory network of the soil microbiom... more Antibiotics entering the soil likely disturb the complex regulatory network of the soil microbiome, which is closely associated with soil quality and ecological function. This study investigated the effects of tetracycline (TC), sulfamonomethoxine (SMM), ciprofloxacin (CIP) and their combination (AM) on the bacterial community in a soil-microbe-plant system and identified the main bacterial responders. Antibiotic effects on the soil microbiome depended on antibiotic type and exposure time. TC resulted in an acute but more rapidly declining effect on soil microbiome while CIP and SMM led to a delayed antibiotic effect. The soil exposed to AM presented a highly similar bacterial structure to that exposed to TC rather than to SMM and CIP. TC, SMM and CIP had their own predominantly impacted taxonomic groups that include both resistance and sensitive bacteria. The antibiotic sensitive responders predominantly distributed within the phylum Proteobacteria. The potential bacteria resistant...
Environmental pollution (Barking, Essex : 1987), Jan 14, 2016
This work investigated the responses of antibiotic resistance genes (ARGs) and the soil microbial... more This work investigated the responses of antibiotic resistance genes (ARGs) and the soil microbial community in a paddy-upland rotation system to mineral fertilizer (NPK) and different application dosages of manure combined with NPK. The occurrence of five tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), two sulfonamide ARGs (sul1 and sul2) and one genetic element (IntI1) was quantified. NPK application showed only slight or no impact on soil ARGs abundances compared with the control without fertilizer. Soil ARGs abundances could be increased by manure-NPK application but was related to manure dosage (2250-9000 kg ha(-1)). Principal component analysis (PCA) showed that the soil ARG profile of the treatment with 9000 kg ha(-1) manure separated clearly from the other treatments; the ARGs that contributed most to the discrimination of this treatment were tetA, tetG, tetW, sul1, sul2 and IntI1. Community level physiological profile (CLPP) analysis showed that increasing manure dosage...
Applied and Environmental Microbiology, Mar 1, 2003
The potential for oxidation of ammonia in anoxic marine sediments exists through anaerobic oxidat... more The potential for oxidation of ammonia in anoxic marine sediments exists through anaerobic oxidation by Nitrosomonas-like organisms, utilizing nitrogen dioxide, coupling of nitrification, manganese reduction, and anaerobic oxidation of ammonium by planctomycetes (the Anammox process). Here we describe the presence of microbial communities with the potential to carry out these processes in a natural marine sediment system (Loch Duich, Scotland). Natural microbial communities of Planctomycetales-Verrucomicrobia and -and ␥-proteobacterial ammonia-oxidizing bacteria were characterized by analysis of 16S rRNA genes amplified using group-specific primers by PCR-and reverse transcription-PCR amplification of 16S rDNA and RNA, respectively. Amplification products were analyzed by sequencing of clones and by denaturant gradient gel electrophoresis (DGGE). Amplification of primers specific for Planctomycetales-Verrucomicrobia and -proteobacterial ammonia-oxidizing bacteria generated products at all sampling sites and depths, but no product was generated using primers specific for ␥-proteobacterial ammonia-oxidizing bacteria. 16S rDNA DGGE banding patterns indicated complex communities of -proteobacterial ammonia-oxidizing bacteria in anoxic marine sediments. Phylogenetic analysis of sequences from clones and those excised from DGGE gels suggests dominance of Nitrosospira cluster 1-like organisms and of strains belonging to a novel cluster represented in dominant bands in 16S rRNA DGGE banding patterns. Their presence indicates a group of organisms closely related to recognized -proteobacterial ammonia-oxidizing bacteria that may be selected in anoxic environments and may be capable of anoxic ammonia oxidation. Sequence analysis of planctomycete clone libraries and sequences excised from DGGE gels also demonstrated a diverse microbial community and suggested the presence of new subdivisions, but no sequence related to recognized Anammox organisms was detected.
The environment disseminates antimicrobial-resistance genes; however, it remains challenging to d... more The environment disseminates antimicrobial-resistance genes; however, it remains challenging to distinguish whether human activities exacerbate antimicrobial resistance or what is natural. Here, we quantified ~300 resistance-related genes in 200+ Scottish soil samples. Location or land use does not explain gene differences, but nutrient levels reduce gene richness. Elevated levels of metals increased gene richness, and selenium increased transposase levels. Rainfall and persistent organic pollutants also increased transposase relative abundance, possibly promoting conditions conducive to the horizontal transfer of antimicrobial-resistance genes. Selenium and polychlorinated biphenyls were primary factors in gene abundance, while polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pH influenced gene diversity. Polychlorinated biphenyls are derived from anthropogenic activities, highlighting human activities’ potential impact on gene prevalence. This is the first national...
One of the main drivers for the recent interest in utilising fungi has been the development of mo... more One of the main drivers for the recent interest in utilising fungi has been the development of molecular technologies which allow us to investigate fungal communities in detail. We have made significant steps forward in understanding numbers and functions of fungal communities in soil. If we are to make progress in harnessing fungal communities for improving the sustainability of our production systems, we need to improve our ability to accurately monitor species composition, abundance and interactions, and to increase our understanding of functional traits. This chapter presents recent advances in the study of these ubiquitous and vital components of all terrestrial ecosystems.
Ammonia oxidation, as the first step in the nitrification process, plays a central role in the gl... more Ammonia oxidation, as the first step in the nitrification process, plays a central role in the global cycling of nitrogen. Although bacteria are traditionally considered to be responsible for ammonia oxidation, a role for archaea has been suggested by data from metagenomic studies and by the isolation of a marine, autotrophic, ammonia-oxidizing, non-thermophilic crenarchaeon. Evidence for ammonia oxidation by non-thermophilic crenarchaea in marine and terrestrial environments is largely based on abundance of bacterial and archaeal ammonia monooxygenase (amo) genes, rather than activity. In this study, we have determined the influence of temperature on the response of ammonia-oxidizing bacteria and archaea in nitrifying soil microcosms using two approaches, involving analysis of transcriptional activity of 16S rRNA genes and of a key functional gene, amoA, which encodes ammonia monooxygenase subunit A. There was little evidence of changes in relative abundance or transcriptional activity of ammoniaoxidizing bacteria during nitrification. In contrast, denaturing gradient gel electrophoresis analysis of crenarchaeal 16S rRNA and crenarchaeal amoA genes provided strong evidence of changes in community structure of active archaeal ammonia oxidizers. Community structure changes were similar during incubation at different temperatures and much of the activity was due to a group of non-thermophilic crenarchaea associated with subsurface and marine environments, rather than soil. The findings suggest a role for crenarchaea in soil nitrification and that further information is required on their biogeography.
The relationship between biogeochemical process rates and microbial functional activity was inves... more The relationship between biogeochemical process rates and microbial functional activity was investigated by analysis of the transcriptional dynamics of the key functional genes for methanogenesis (methyl coenzyme M reductase; mcrA) and methane oxidation (particulate methane monooxygenase; pmoA) and in situ methane flux at two peat soil field sites with contrasting net methane-emitting and -oxidizing characteristics. qPCR was used to quantify the abundances of mcrA and pmoA genes and transcripts at two soil depths. Total methanogen and methanotroph transcriptional dynamics, calculated from mcrA and pmoA gene : transcript abundance ratios, were similar at both sites and depths. However, a linear relationship was demonstrated between surface mcrA and pmoA transcript dynamics and surface flux rates at the methane-emitting and methane-oxidizing sites, respectively. Results indicate that methanotroph activity was at least partially substrate-limited at the methane-emitting site and by oth...
Pasteuria spp. are endospore forming bacteria which act as natural antagonists to many of the mos... more Pasteuria spp. are endospore forming bacteria which act as natural antagonists to many of the most economically significant plant parasitic nematodes (PPNs). Highly speciesspecific nematode suppression may be observed in soils containing a sufficiently high density of Pasteuria spp. spores. This suppression is enacted by the bacteria via inhibition of root invasion and sterilization of the nematode host. Molecular methods for the detection of Pasteuria spp. from environmental DNA (eDNA) have been described; however, these methods are limited in both scale and in depth. We report the use of small subunit rRNA gene metabarcoding to profile Pasteuria spp. and nematode communities in parallel. We have investigated Pasteuria spp. population structure in Scottish soils using eDNA from two sources: soil extracted DNA from the second National Soil Inventory of Scotland (NSIS2); and nematode extracted DNA collected from farms in the East Scotland Farm Network (ESFN). We compared the Pasteuria spp. community culture to both nematode community structure and the physiochemical properties of soils. Our results indicate that Pasteuria spp. populations in Scottish soils are broadly dominated by two sequence variants. The first of these aligns with high identity to Pasteuria hartismeri, a species first described parasitizing Meloidogyne ardenensis, a nematode parasite of woody and perennial plants in northern Europe. The second aligns with a Pasteuria-like sequence which was first recovered from a farm near Edinburgh which was found to contain bacterial feeding nematodes and Pratylenchus spp. encumbered by Pasteuria spp. endospores. Further, soil carbon, moisture, bulk density, and pH showed a strong correlation with the Pasteuria spp. community composition. These results indicate that metabarcoding is appropriate for the sensitive, specific, and semi-quantitative profiling of Pasteuria species from eDNA.
Streams and rivers are an important source of CO 2 emissions 1. One important control of these em... more Streams and rivers are an important source of CO 2 emissions 1. One important control of these emissions is the metabolic balance between photosynthesis, which converts CO 2 to organic carbon, and respiration, which converts organic carbon into CO 2 (refs 2,3). Carbon emissions from rivers could increase with warming, independently of organic carbon inputs, because the apparent activation energy is predicted to be higher for respiration than photosynthesis 4,5. However, physiological CO 2-concentrating mechanisms may prevent the increase in photorespiration, limiting photosynthesis with warming 6. Here we report the thermal response of aquatic photosynthesis from streams located in geothermal areas of North America, Iceland and Kamchatka with water temperatures ranging between 4 and 70 • C. Based on a thermodynamic theory of enzyme kinetics, we show that the apparent activation energy of aquatic ecosystem photosynthesis is approximately 0.57 electron volts (eV) for temperatures ranging from 4 to 45 • C, which is similar to that of respiration 4,5,7-9. This result and a global synthesis of 222 streams suggest that warming will not create increased stream and river CO 2 emissions from a warming-induced imbalance between photosynthesis and respiration. However, temperature could a ect annual CO 2 emissions from streams if ecosystem respiration is independent of gross primary production, and may be amplified by increasing organic carbon supply. A key, rate-limiting step during photosynthesis is CO 2-fixing by the D-ribulose-1,5-bisphosphate carboxylase/oxygenase enzyme (Rubisco) 10,11. The average activation energy of Rubisco carboxylase activity across phylogenetic groups is about 0.57 eV (chlorophytes 0.30 eV, cyanobacteria 0.44 eV, spermatophytes 0.63 eV, diatoms 0.65 eV, rhodophytes 0.82 eV) (refs 12,13) and is similar to the respiratory complex, but it becomes less efficient with warming under the decreasing solubility of CO 2 /O 2 concentration ratio in solution leading to photorespiration (fixation of O 2 instead of CO 2) (refs 10,11,14). This creates a difference in apparent (or effective) activation energies between photosynthesis (E a ≈ 0.32 eV, based on C3 terrestrial plant metabolism) 10 and community respiration (E cr ≈ 0.47 to 0.65 eV) (refs 4,5,7-9) predicted to alter the metabolic balance of aquatic ecosystems in response to warming 4,5,15. However, most autotrophic aquatic organisms, contributing to half of the global oxygenic photosynthesis 16 , have evolved a diversity
This study provided an assessment of the environmental fate of antibiotic resistance genes (ARGs)... more This study provided an assessment of the environmental fate of antibiotic resistance genes (ARGs) in a Scottish grassland field repeatedly treated with different organic fertilizers. The impacts of manure, biosolids and municipal food-derived compost on the relative abundances of tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), sulfonamide ARGs (sul1 and sul2) and class 1 integron-integrase gene (IntI1) in soils were investigated, with inorganic fertilizer (NPK) as a comparison. The background soil with a history of low intensity farming showed a higher total relative abundance of tet ARGs over sul ARGs, with tetracycline efflux genes occurring in a higher frequency. In all treatments, the relative abundances of most ARGs detected in soils decreased over time, especially IntI1 and tet ARGs. This general attenuation of soil ARGs is a reflection of changes in the soil microbial community, which is supported by the result that almost all the soils at the end of the experiment had different bacterial communities from the untreated soil at the beginning of the experiment. Multiple applications of organic fertilizers to some extent counteracted the decreasing trend of soil ARGs relative abundances, which resulted in higher ARGs relative abundances in comparison to NPK, either by a lesser decrease of IntI1 and tet ARGs or an increase of sul ARGs. The enhancement of existing soil ARG prevalence by organic fertilizers was strongly dependent on the organic fertilizer type and the particular ARG. Compost contained the lowest relative abundance of inherent ARGs and had the least effect on the soil ARG decrease after application. The relative increase of tet ARGs caused by biosolids was larger than that of sul ARGs, while manure caused the opposite effect. Fertilization practices did not exert effective impacts on the soil bacterial community, although it caused significant changes in the profile of the ARG pool. Organic fertilization may thus accelerate the dissemination of ARGs in soil mainly through horizontal gene transfer (HGT), consistent with the enrichment of IntI1 in organic fertilized soils.
It is well established that resource quantity and elemental stoichiometry play major roles in sha... more It is well established that resource quantity and elemental stoichiometry play major roles in shaping below and aboveground plant biodiversity, but their importance for shaping microbial diversity in soil remains unclear. Here, we used statistical modeling on a regional database covering 179 locations and six ecosystem types across Scotland to evaluate the roles of total carbon (C), nitrogen (N) and phosphorus (P) availabilities and ratios, together with land use, climate and biotic and abiotic factors, in determining regional scale patterns of soil bacterial diversity. We found that bacterial diversity and composition were primarily driven by variation in soil resource stoichiometry (total C:N:P ratios), itself linked to different land uses, and secondarily driven by other important biodiversity drivers such as climate, soil spatial heterogeneity, soil pH, root influence (plant-soil microbe interactions) and microbial biomass (soil microbe-microbe interactions). In aggregate, these...
Rising global temperatures may increase the rates of soil organic matter decomposition by heterot... more Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO 2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor PLOS ONE |
Environmental pollution (Barking, Essex : 1987), Jan 4, 2016
Antibiotics entering the soil likely disturb the complex regulatory network of the soil microbiom... more Antibiotics entering the soil likely disturb the complex regulatory network of the soil microbiome, which is closely associated with soil quality and ecological function. This study investigated the effects of tetracycline (TC), sulfamonomethoxine (SMM), ciprofloxacin (CIP) and their combination (AM) on the bacterial community in a soil-microbe-plant system and identified the main bacterial responders. Antibiotic effects on the soil microbiome depended on antibiotic type and exposure time. TC resulted in an acute but more rapidly declining effect on soil microbiome while CIP and SMM led to a delayed antibiotic effect. The soil exposed to AM presented a highly similar bacterial structure to that exposed to TC rather than to SMM and CIP. TC, SMM and CIP had their own predominantly impacted taxonomic groups that include both resistance and sensitive bacteria. The antibiotic sensitive responders predominantly distributed within the phylum Proteobacteria. The potential bacteria resistant...
Environmental pollution (Barking, Essex : 1987), Jan 14, 2016
This work investigated the responses of antibiotic resistance genes (ARGs) and the soil microbial... more This work investigated the responses of antibiotic resistance genes (ARGs) and the soil microbial community in a paddy-upland rotation system to mineral fertilizer (NPK) and different application dosages of manure combined with NPK. The occurrence of five tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), two sulfonamide ARGs (sul1 and sul2) and one genetic element (IntI1) was quantified. NPK application showed only slight or no impact on soil ARGs abundances compared with the control without fertilizer. Soil ARGs abundances could be increased by manure-NPK application but was related to manure dosage (2250-9000 kg ha(-1)). Principal component analysis (PCA) showed that the soil ARG profile of the treatment with 9000 kg ha(-1) manure separated clearly from the other treatments; the ARGs that contributed most to the discrimination of this treatment were tetA, tetG, tetW, sul1, sul2 and IntI1. Community level physiological profile (CLPP) analysis showed that increasing manure dosage...
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Papers by Thomas Freitag