Donal Eardly - Profile on Academia.edu (original) (raw)
Papers by Donal Eardly
Earth and Planetary Science Letters, 1998
Elevated microbial biomass levels play a significant role in altering the chemical composition of... more Elevated microbial biomass levels play a significant role in altering the chemical composition of hydrothermal plumes. In this work, a procedure was developed for collecting sufficient quantities of microbial biomass from a hydrothermal plume to allow the extraction of DNA suitable for use in molecular analyses of the plume microbial populations. During a geophysical survey along 200 km of the Mid-Atlantic Ridge (MAR), southwest of the Azores Triple Junction, several new sites of hydrothermal activity were identified, including the Rainbow hydrothermal plume, at 36º15 0 N, the strongest such feature yet reported from the MAR. During the survey, in situ filtration systems were used to collect microbial biomass from the water column onto 293 mm diameter, 0.2 µm-pore membrane filters by pumping large volumes (300-500 l) of seawater through the filters. Filter samples were collected from both the neutrally buoyant portion of the Rainbow plume (at a depth of 2050 m) and from above it in the water column (at 1500 m). Microgram quantities of genomic DNA were extracted and purified from the biomass on these filters. The suitability of the purified DNA for use in molecular analyses was demonstrated by polymerase chain reaction (PCR) amplification of the small subunit ribosomal rRNA (SSU rRNA) gene from the two primary prokaryotic domains, the Bacteria and the Archaea. As indicated by the binding of domain-specific oligonucleotide hybridisation probes to the purified DNA, the plume microbial populations contained a higher proportion of members of the domain Archaea than the populations in the surrounding ambient sea-water. cles in the oceans, with hydrothermal fluxes a major carrier of heat and mass to the oceans from freshformed underlying oceanic crust . Hydrothermal plumes represent the ultimate fate of the majority of the hydrothermal discharge and, thus, are of fundamental importance in determining the net impact of hydrothermal activity on global ocean budgets. Hydrothermal plumes are generated when hydrother-0012-821X/98/$19.00 © 1998 Elsevier Science B.V. All rights reserved. PII S 0 0 1 2 -8 2 1 X ( 9 8 ) 0 0 0 3 7 -5
Progress in Oceanography, 2001
Results are presented from four cruises to the Porcupine Abyssal Plain (PAP site) that took place... more Results are presented from four cruises to the Porcupine Abyssal Plain (PAP site) that took place during the BENGAL project from September 1996 to March 1998, and two cruises to the PAP and an oligotrophic site (EUMELI) that took place during the DEEPSEAS project between September 1993 and March 1994. Bacterial abundances in sediment and sediment contact water were measured by epifluorescence microscopy. Bacterial activity was determined by 3H-thymidine incorporation as a measure of DNA synthesis, and by 3H-leucine incorporation as a measure of protein synthesis. Activities were measured under atmospheric and in situ pressures and temperatures. Bacterial activity was usually higher in samples incubated at in situ pressure than those incubated at atmospheric pressure indicating that a barophilic community was dominant. Inter-cruise comparisons of abundance and activity during the BENGAL project showed no firm evidence of there being a seasonal response in the benthic microbial community to any episodic phytodetritus event. This was probably because of inter-annual variations in the quality and quantity of phytodetritus deposition at the PAP site, the rapid remineralization of fresh organic material by the microbial communities and the timing of cruises to the study area. 3H-thymidine and 3H-leucine incorporation in sediments was higher during the BENGAL period than the DEEPSEAS programme. A methodological change in the 3H-thymidine incorporation technique for sediments may explain the differences in DNA synthesis observed between the two projects, whereas the lower levels of protein synthesis observed during the DEEPSEAS programme probably reflected both inter-annual variations in activity at the PAP site and the lower productivity that prevailed at surface at the EUMELI oligotrophic site. Rates of 3H-thymidine incorporation in sediment contact water were similar during both projects.
Deep-sea Research Part I-oceanographic Research Papers, 1997
Bacterial biomass and activity were investigated in deep waters at two sites in the eastern Atlan... more Bacterial biomass and activity were investigated in deep waters at two sites in the eastern Atlantic, of similar depth (4560–4800 m), but varying in their nutritional status. The Northern (N) site was eutrophic and subject to a strong seasonal input of surface derived organic matter (phytodetritus) to the sediment. The Southern (S) site was oligotrophic. Deep water at this site does not appear to receive any strong seasonal input. Bacterial numbers in the deep water column at the N site showed no significant seasonal variation but were greater than those at the S site. Deep water bacteria were typically small and free-living. From biovolume determinations, it was estimated that mean concentrations of bacterial organic carbon at depths greater than 500 m were 0.12 (0.03–0.29) μg C 1−1 and 0.02 (0.01–0.04) μg C 1−1 at the N and S sites, respectively. Rates of thymidine and leucine incorporation were used as indicators of bacterial activity. Bacterial communities in water in contact with the sediment (SCW; sediment contact water) at both sites (but especially at the S site) were strongly barophilic at in situ temperatures (2.5–4.1°C). The barophilic response of thymidine incorporation was enhanced when SCW samples from the N site were incubated at 11.5°C. It is proposed that this result indicated an elevating effect of pressure on cardinal temperatures and that the SCW community was obligately psychrophilic when unpressurised. Comparison of cell-specific incorporation rates determined under in situ conditions showed bacteria in the SCW to have levels of activity comparable with bacteria from a depth of 150 m. Thymidine incorporation rates were highest in SCW samples taken at the N site in May 1988 and September 1989. Thymidine incorporation by SCW samples taken immediately before (10 April 1994) the main spring-bloom-associated deposition of phytodetritus was significantly lower and comparable with that determined for the oligotrophic S site. The attributes exhibited by the SCW community appeared to be highly localised. We conclude that the bacterial communities of the SCW are active and adapted to their environment. Activity is influenced by the trophic nature of the site and may show temporal changes linked with episodic food supply. We postulate that the existence of such communities is linked to the role of the sediment-water interface as the initial site of deposition of sea-surface derived labile organic material.
Water Research, 2004
The diversity, population dynamics, and activity profiles of methanogens in anaerobic granular sl... more The diversity, population dynamics, and activity profiles of methanogens in anaerobic granular sludges from two anaerobic hybrid reactors treating a molasses wastewater both mesophilically (37°C) and thermophilically (55°C) during a 1081 day trial were determined. The influent to one of the reactors was supplemented with sulphate, after an acclimation period of 112 days, to determine the effect of competition with sulphate-reducing bacteria on the methanogenic community structure. Sludge samples were removed from the reactors at intervals throughout the operational period and examined by amplified ribosomal DNA (rDNA) restriction analysis (ARDRA) and partial sequencing of 16S rRNA genes. In total, 18 operational taxonomic units (OTUs) were identified, 12 of which were sequenced. The methanogenic communities in both reactors changed during the operational period. The seed sludge and the reactor biomass sampled during mesophilic operation, both in the presence and absence of sulphate, was characterised by a predominance of Methanosaeta spp. Following temperature elevation, the dominant methanogenic sequences detected in the non-sulphate supplemented reactor were closely related to Methanocorpusculum parvum. By contrast, the dominant OTUs detected in the sulphate-supplemented reactor upon temperature increase were related to the hydrogen-utilising methanogen, Methanobacterium thermoautotrophicum. The observed methanogenic community structure in the reactors correlated with the operational performance of the reactors during the trial and with physiological measurements of the reactor biomass. Both reactors achieved chemical oxygen demand (COD) removal efficiencies of over 90% during mesophilic operation, with or without sulphate supplementation. During thermophilic operation, the presence of sulphate resulted in decreased reactor performance (effluent acetate concentrations of >3000 mg/l and biogas methane content of <25%). It was demonstrated that methanogenic conversion of acetate at 55°C was extremely sensitive to inhibition by sulphide (50% inhibition at 8–17 mg/l unionised sulphide at pH 7.6–8.0), while the conversion of H2/CO2 methanogenically was favoured. The combination of experiments carried out demonstrated the presence of specific methanogenic populations during periods of successful operational performance.
Progress in Oceanography, 2001
This paper describes inter-specific differences in the distribution of sediment in the gut compar... more This paper describes inter-specific differences in the distribution of sediment in the gut compartments and in the enzyme and bacterial profiles along the gut of abyssal holothurian species — Oneirophanta mutabilis, Psychropotes longicauda and Pseudostichopus villosus sampled from a eutrophic site in the NE Atlantic at different times of the year. Proportions of sediments, relative to total gut contents, in the pharynx, oesophagus, anterior and posterior intestine differed significantly in all the inter-species comparisons, but not between inter-seasonal comparisons. Significant differences were also found between the relative proportions of sediments in both the rectum and cloaca of Psychropotes longicauda and Oneirophanta mutabilis. Nineteen enzymes were identified in either gut-tissue or gut-content samples of the holothurians studied. Concentrations of the enzymes in gut tissues and their contents were highly correlated. Greater concentrations of the enzymes were found in the gut tissues suggesting that they are the main source of the enzymes. The suites of enzymes recorded were broadly similar in each of the species sampled collected regardless of the time of the year, and they were similar to those described previously for shallow-water holothurians. Significant inter-specific differences in the gut tissue concentrations of some of the glycosidases suggest dietary differences. For example, Psychropotes longicauda and Pseudostichopus villosus contain higher levels of chitobiase than Oneirophanta mutabilis. There were no seasonal changes in bacterial activity profiles along the guts of O. mutabilis and Pseudostichopus villosus. In both these species bacterial activity and abundance declined between the pharynx/oesophagus and anterior intestine, but then increased along the gut and became greatest in the rectum/cloaca. Although the data sets were more limited for Psychropotes longicauda, bacterial activity increased from the anterior to the posterior intestine but then declined slightly to the rectum/cloaca. These changes in bacterial activity and densities probably reflect changes in the microbial environment along the guts of abyssal holothurians. Such changes suggest that there is potential for microbial breakdown of a broader range of substrates than could be otherwise be achieved by the holothurian itself. However, the present study found no evidence for sedimentary (microbial) sources of hydrolytic enzymes.
FEMS Microbiology Ecology, 2000
This work describes the microbial community structure in the water column at the Porcupine Abyssa... more This work describes the microbial community structure in the water column at the Porcupine Abyssal Plain in the eastern North Atlantic. Restriction fragment length polymorphism analysis was carried out on clone libraries constructed from samples collected at 100 m, 1000 m, 3000 m, 10 m above bottom and sediment contact water during July 1997 and March 1998. Simpson (1/D) and Shannon (HP) diversity indices revealed temporal and spatial variations in the community structure and complexity. Higher diversity was observed in the samples collected from 100 m (HP = 3.22), 1000 m (HP = 3.48) and 10 m above bottom (HP = 3.18) during July 1997 compared with the corresponding samples during March 1998. Changes in diversity may be associated with a seasonal flux in particulate organic matter. This could promote the proliferation of a selection of taxa that are adapted to rapidly responding to a large influx of organic matter. Sequencing of clones representing 20 operational taxonomic units revealed a diverse population of Bacteria and Archaea. The most numerous clone operational taxonomic units were from the K and Q subdivisions of the Proteobacteria and the group I marine Crenarchaeota. A number of sequences were phylogenetically grouped in clades with no culture representatives such as the SAR116, SAR86, SAR406 and SAR324 groups. Most of the sequences identified were found to be more closely related to other 16S rDNA clones recovered from the marine environment rather than cultured species.
Extraction of prokaryotic genomic DNA from marine microbial communities suitable for amplification using the polymerase chain reaction
Internationale Revue der gesamten Hydrobiologie und Hydrographie, 1995
Abstract We present a method for extraction of DNA from marine microbial communities and amplific... more Abstract We present a method for extraction of DNA from marine microbial communities and amplification of the small subunit ribosomal RNA gene from the prokaryotic organisms contained therein. Results of cloning, sequencing and phylogenetic analyses are also presented. This DNA extraction technique is specifically designed to be used in conjunction with the Polymerase Chain Reaction (PCR). Emphasis was placed on producing a technique which results in total cell lysis yielding DNA of sufficient purity to facilitate ...
Earth and Planetary Science Letters, 1998
Elevated microbial biomass levels play a significant role in altering the chemical composition of... more Elevated microbial biomass levels play a significant role in altering the chemical composition of hydrothermal plumes. In this work, a procedure was developed for collecting sufficient quantities of microbial biomass from a hydrothermal plume to allow the extraction of DNA suitable for use in molecular analyses of the plume microbial populations. During a geophysical survey along 200 km of the Mid-Atlantic Ridge (MAR), southwest of the Azores Triple Junction, several new sites of hydrothermal activity were identified, including the Rainbow hydrothermal plume, at 36º15 0 N, the strongest such feature yet reported from the MAR. During the survey, in situ filtration systems were used to collect microbial biomass from the water column onto 293 mm diameter, 0.2 µm-pore membrane filters by pumping large volumes (300-500 l) of seawater through the filters. Filter samples were collected from both the neutrally buoyant portion of the Rainbow plume (at a depth of 2050 m) and from above it in the water column (at 1500 m). Microgram quantities of genomic DNA were extracted and purified from the biomass on these filters. The suitability of the purified DNA for use in molecular analyses was demonstrated by polymerase chain reaction (PCR) amplification of the small subunit ribosomal rRNA (SSU rRNA) gene from the two primary prokaryotic domains, the Bacteria and the Archaea. As indicated by the binding of domain-specific oligonucleotide hybridisation probes to the purified DNA, the plume microbial populations contained a higher proportion of members of the domain Archaea than the populations in the surrounding ambient sea-water. cles in the oceans, with hydrothermal fluxes a major carrier of heat and mass to the oceans from freshformed underlying oceanic crust . Hydrothermal plumes represent the ultimate fate of the majority of the hydrothermal discharge and, thus, are of fundamental importance in determining the net impact of hydrothermal activity on global ocean budgets. Hydrothermal plumes are generated when hydrother-0012-821X/98/$19.00 © 1998 Elsevier Science B.V. All rights reserved. PII S 0 0 1 2 -8 2 1 X ( 9 8 ) 0 0 0 3 7 -5
Progress in Oceanography, 2001
Results are presented from four cruises to the Porcupine Abyssal Plain (PAP site) that took place... more Results are presented from four cruises to the Porcupine Abyssal Plain (PAP site) that took place during the BENGAL project from September 1996 to March 1998, and two cruises to the PAP and an oligotrophic site (EUMELI) that took place during the DEEPSEAS project between September 1993 and March 1994. Bacterial abundances in sediment and sediment contact water were measured by epifluorescence microscopy. Bacterial activity was determined by 3H-thymidine incorporation as a measure of DNA synthesis, and by 3H-leucine incorporation as a measure of protein synthesis. Activities were measured under atmospheric and in situ pressures and temperatures. Bacterial activity was usually higher in samples incubated at in situ pressure than those incubated at atmospheric pressure indicating that a barophilic community was dominant. Inter-cruise comparisons of abundance and activity during the BENGAL project showed no firm evidence of there being a seasonal response in the benthic microbial community to any episodic phytodetritus event. This was probably because of inter-annual variations in the quality and quantity of phytodetritus deposition at the PAP site, the rapid remineralization of fresh organic material by the microbial communities and the timing of cruises to the study area. 3H-thymidine and 3H-leucine incorporation in sediments was higher during the BENGAL period than the DEEPSEAS programme. A methodological change in the 3H-thymidine incorporation technique for sediments may explain the differences in DNA synthesis observed between the two projects, whereas the lower levels of protein synthesis observed during the DEEPSEAS programme probably reflected both inter-annual variations in activity at the PAP site and the lower productivity that prevailed at surface at the EUMELI oligotrophic site. Rates of 3H-thymidine incorporation in sediment contact water were similar during both projects.
Deep-sea Research Part I-oceanographic Research Papers, 1997
Bacterial biomass and activity were investigated in deep waters at two sites in the eastern Atlan... more Bacterial biomass and activity were investigated in deep waters at two sites in the eastern Atlantic, of similar depth (4560–4800 m), but varying in their nutritional status. The Northern (N) site was eutrophic and subject to a strong seasonal input of surface derived organic matter (phytodetritus) to the sediment. The Southern (S) site was oligotrophic. Deep water at this site does not appear to receive any strong seasonal input. Bacterial numbers in the deep water column at the N site showed no significant seasonal variation but were greater than those at the S site. Deep water bacteria were typically small and free-living. From biovolume determinations, it was estimated that mean concentrations of bacterial organic carbon at depths greater than 500 m were 0.12 (0.03–0.29) μg C 1−1 and 0.02 (0.01–0.04) μg C 1−1 at the N and S sites, respectively. Rates of thymidine and leucine incorporation were used as indicators of bacterial activity. Bacterial communities in water in contact with the sediment (SCW; sediment contact water) at both sites (but especially at the S site) were strongly barophilic at in situ temperatures (2.5–4.1°C). The barophilic response of thymidine incorporation was enhanced when SCW samples from the N site were incubated at 11.5°C. It is proposed that this result indicated an elevating effect of pressure on cardinal temperatures and that the SCW community was obligately psychrophilic when unpressurised. Comparison of cell-specific incorporation rates determined under in situ conditions showed bacteria in the SCW to have levels of activity comparable with bacteria from a depth of 150 m. Thymidine incorporation rates were highest in SCW samples taken at the N site in May 1988 and September 1989. Thymidine incorporation by SCW samples taken immediately before (10 April 1994) the main spring-bloom-associated deposition of phytodetritus was significantly lower and comparable with that determined for the oligotrophic S site. The attributes exhibited by the SCW community appeared to be highly localised. We conclude that the bacterial communities of the SCW are active and adapted to their environment. Activity is influenced by the trophic nature of the site and may show temporal changes linked with episodic food supply. We postulate that the existence of such communities is linked to the role of the sediment-water interface as the initial site of deposition of sea-surface derived labile organic material.
Water Research, 2004
The diversity, population dynamics, and activity profiles of methanogens in anaerobic granular sl... more The diversity, population dynamics, and activity profiles of methanogens in anaerobic granular sludges from two anaerobic hybrid reactors treating a molasses wastewater both mesophilically (37°C) and thermophilically (55°C) during a 1081 day trial were determined. The influent to one of the reactors was supplemented with sulphate, after an acclimation period of 112 days, to determine the effect of competition with sulphate-reducing bacteria on the methanogenic community structure. Sludge samples were removed from the reactors at intervals throughout the operational period and examined by amplified ribosomal DNA (rDNA) restriction analysis (ARDRA) and partial sequencing of 16S rRNA genes. In total, 18 operational taxonomic units (OTUs) were identified, 12 of which were sequenced. The methanogenic communities in both reactors changed during the operational period. The seed sludge and the reactor biomass sampled during mesophilic operation, both in the presence and absence of sulphate, was characterised by a predominance of Methanosaeta spp. Following temperature elevation, the dominant methanogenic sequences detected in the non-sulphate supplemented reactor were closely related to Methanocorpusculum parvum. By contrast, the dominant OTUs detected in the sulphate-supplemented reactor upon temperature increase were related to the hydrogen-utilising methanogen, Methanobacterium thermoautotrophicum. The observed methanogenic community structure in the reactors correlated with the operational performance of the reactors during the trial and with physiological measurements of the reactor biomass. Both reactors achieved chemical oxygen demand (COD) removal efficiencies of over 90% during mesophilic operation, with or without sulphate supplementation. During thermophilic operation, the presence of sulphate resulted in decreased reactor performance (effluent acetate concentrations of >3000 mg/l and biogas methane content of <25%). It was demonstrated that methanogenic conversion of acetate at 55°C was extremely sensitive to inhibition by sulphide (50% inhibition at 8–17 mg/l unionised sulphide at pH 7.6–8.0), while the conversion of H2/CO2 methanogenically was favoured. The combination of experiments carried out demonstrated the presence of specific methanogenic populations during periods of successful operational performance.
Progress in Oceanography, 2001
This paper describes inter-specific differences in the distribution of sediment in the gut compar... more This paper describes inter-specific differences in the distribution of sediment in the gut compartments and in the enzyme and bacterial profiles along the gut of abyssal holothurian species — Oneirophanta mutabilis, Psychropotes longicauda and Pseudostichopus villosus sampled from a eutrophic site in the NE Atlantic at different times of the year. Proportions of sediments, relative to total gut contents, in the pharynx, oesophagus, anterior and posterior intestine differed significantly in all the inter-species comparisons, but not between inter-seasonal comparisons. Significant differences were also found between the relative proportions of sediments in both the rectum and cloaca of Psychropotes longicauda and Oneirophanta mutabilis. Nineteen enzymes were identified in either gut-tissue or gut-content samples of the holothurians studied. Concentrations of the enzymes in gut tissues and their contents were highly correlated. Greater concentrations of the enzymes were found in the gut tissues suggesting that they are the main source of the enzymes. The suites of enzymes recorded were broadly similar in each of the species sampled collected regardless of the time of the year, and they were similar to those described previously for shallow-water holothurians. Significant inter-specific differences in the gut tissue concentrations of some of the glycosidases suggest dietary differences. For example, Psychropotes longicauda and Pseudostichopus villosus contain higher levels of chitobiase than Oneirophanta mutabilis. There were no seasonal changes in bacterial activity profiles along the guts of O. mutabilis and Pseudostichopus villosus. In both these species bacterial activity and abundance declined between the pharynx/oesophagus and anterior intestine, but then increased along the gut and became greatest in the rectum/cloaca. Although the data sets were more limited for Psychropotes longicauda, bacterial activity increased from the anterior to the posterior intestine but then declined slightly to the rectum/cloaca. These changes in bacterial activity and densities probably reflect changes in the microbial environment along the guts of abyssal holothurians. Such changes suggest that there is potential for microbial breakdown of a broader range of substrates than could be otherwise be achieved by the holothurian itself. However, the present study found no evidence for sedimentary (microbial) sources of hydrolytic enzymes.
FEMS Microbiology Ecology, 2000
This work describes the microbial community structure in the water column at the Porcupine Abyssa... more This work describes the microbial community structure in the water column at the Porcupine Abyssal Plain in the eastern North Atlantic. Restriction fragment length polymorphism analysis was carried out on clone libraries constructed from samples collected at 100 m, 1000 m, 3000 m, 10 m above bottom and sediment contact water during July 1997 and March 1998. Simpson (1/D) and Shannon (HP) diversity indices revealed temporal and spatial variations in the community structure and complexity. Higher diversity was observed in the samples collected from 100 m (HP = 3.22), 1000 m (HP = 3.48) and 10 m above bottom (HP = 3.18) during July 1997 compared with the corresponding samples during March 1998. Changes in diversity may be associated with a seasonal flux in particulate organic matter. This could promote the proliferation of a selection of taxa that are adapted to rapidly responding to a large influx of organic matter. Sequencing of clones representing 20 operational taxonomic units revealed a diverse population of Bacteria and Archaea. The most numerous clone operational taxonomic units were from the K and Q subdivisions of the Proteobacteria and the group I marine Crenarchaeota. A number of sequences were phylogenetically grouped in clades with no culture representatives such as the SAR116, SAR86, SAR406 and SAR324 groups. Most of the sequences identified were found to be more closely related to other 16S rDNA clones recovered from the marine environment rather than cultured species.
Extraction of prokaryotic genomic DNA from marine microbial communities suitable for amplification using the polymerase chain reaction
Internationale Revue der gesamten Hydrobiologie und Hydrographie, 1995
Abstract We present a method for extraction of DNA from marine microbial communities and amplific... more Abstract We present a method for extraction of DNA from marine microbial communities and amplification of the small subunit ribosomal RNA gene from the prokaryotic organisms contained therein. Results of cloning, sequencing and phylogenetic analyses are also presented. This DNA extraction technique is specifically designed to be used in conjunction with the Polymerase Chain Reaction (PCR). Emphasis was placed on producing a technique which results in total cell lysis yielding DNA of sufficient purity to facilitate ...