title: Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility

authors: Grzymski, Joseph J.

subjects: Epsilonproteobacteria

abstract: Hydrothermal vent ecosystems support diverse life forms, many of which rely on symbiotic associations to perform functions integral to survival in these extreme physicochemical environments. Epsilonproteobacteria, found free-living and in intimate associations with vent invertebrates, are the predominant vent-associated microorganisms. The vent-associated polychaete worm, Alvinella pompejana, is host to a visibly dense fleece of episymbionts on its dorsal surface. The episymbionts are a multispecies consortium of Epsilonproteobacteria present as a biofilm. We unraveled details of these enigmatic, uncultivated episymbionts using environmental genome sequencing. They harbor wide-ranging adaptive traits that include high levels of strain variability analogous to Epsilonproteobacteria pathogens such as Helicobacter pylori, metabolic diversity of free-living bacteria, and numerous orthologs of proteins that we hypothesize are each optimally adapted to specific temperature ranges within the 10–65 °C fluctuations characteristic of the A. pompejana habitat. This strategic combination enables the consortium to thrive under diverse thermal and chemical regimes. The episymbionts are metabolically tuned for growth in hydrothermal vent ecosystems with genes encoding the complete rTCA cycle, sulfur oxidation, and denitrification; in addition, the episymbiont metagenome also encodes capacity for heterotrophic and aerobic metabolisms. Analysis of the environmental genome suggests that A. pompejana may benefit from the episymbionts serving as a stable source of food and vitamins. The success of Epsilonproteobacteria as episymbionts in hydrothermal vent ecosystems is a product of adaptive capabilities, broad metabolic capacity, strain variance, and virulent traits in common with pathogens.

text: Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility Hydrothermal vent ecosystems support diverse life forms, many of which rely on symbiotic associations to perform functions integral to survival in these extreme physicochemical environments. Epsilonproteobacteria, found free-living and in intimate associations with vent invertebrates, are the predominant vent-associated microorganisms. The vent-associated polychaete worm, Alvinella pompejana, is host to a visibly dense fleece of episymbionts on its dorsal surface. The episymbionts are a multispecies consortium of Epsilonproteobacteria present as a biofilm. We unraveled details of these enigmatic, uncultivated episymbionts using environmental genome sequencing. They harbor wide-ranging adaptive traits that include high levels of strain variability analogous to Epsilonproteobacteria pathogens such as Helicobacter pylori, metabolic diversity of free-living bacteria, and numerous orthologs of proteins that we hypothesize are each optimally adapted to specific temperature ranges within the 10–65 °C fluctuations characteristic of the A. pompejana habitat. This strategic combination enables the consortium to thrive under diverse thermal and chemical regimes. The episymbionts are metabolically tuned for growth in hydrothermal vent ecosystems with genes encoding the complete rTCA cycle, sulfur oxidation, and denitrification; in addition, the episymbiont metagenome also encodes capacity for heterotrophic and aerobic metabolisms. Analysis of the environmental genome suggests that A. pompejana may benefit from the episymbionts serving as a stable source of food and vitamins. The success of Epsilonproteobacteria as episymbionts in hydrothermal vent ecosystems is a product of adaptive capabilities, broad metabolic capacity, strain variance, and virulent traits in common with pathogens.

year: 2008

title: Microbial succession under freeze–thaw events and its potential for hydrocarbon degradation in nutrient-amended Antarctic soil

authors: de Jesus, HE

subjects: Science & Technology

abstract: The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes. ◦ ◦

text: Microbial succession under freeze–thaw events and its potential for hydrocarbon degradation in nutrient-amended Antarctic soil The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes. ◦ ◦

year: 2021-03-01

title: Two-step human−environmental impact history for northern New Zealand linked to late-Holocene climate change

authors: Newnham, Rewi M.

subjects: New Zealand

abstract: Following resolution of a long-standing debate over the timing of the initial settlement of New Zealand from Polynesia (late 13th century), a prevailing paradigm has developed that invokes rapid transformation of the landscape, principally by fire, within a few decades of the first arrivals. This model has been constructed from evidence mostly from southern and eastern regions of New Zealand, but a more complicated pattern may apply in the more humid western and northern regions where forests are more resilient to burning. We present a new pollen record from Lake Pupuke, Auckland, northern New Zealand, that charts the changing vegetation cover over the last 1000 years, before and after the arrival of people. Previous results from this site concurred with the rapid transformation model, although sampling resolution, chronology and sediment disturbance make that interpretation equivocal. Our new record is dated principally by tephrochronology together with radiocarbon dating, and includes a cryptotephra deposit identified as Kaharoa tephra, a key marker for first settlement in northern New Zealand. Its discovery and stratigraphic position below two Rangitoto-derived tephras enables a clearer picture of environmental change to be drawn. The new pollen record shows an early phase (step 1) of minor, localised forest clearance around the time of Kaharoa tephra (c. 1314 AD) followed by a later, more extensive deforestation phase (step 2) commencing at around the time of deposition of the Rangitoto tephras (c. 1400‒1450 AD). This pattern, which needs to be corroborated from other well-resolved records from northern New Zealand, concurs with an emerging hypothesis that the ‘Little Ice Age’ had a significant impact on pre-European Māori with the onset of harsher conditions causing a consolidation of populations and later environmental impact in northern New Zealand.

text: Two-step human−environmental impact history for northern New Zealand linked to late-Holocene climate change Following resolution of a long-standing debate over the timing of the initial settlement of New Zealand from Polynesia (late 13th century), a prevailing paradigm has developed that invokes rapid transformation of the landscape, principally by fire, within a few decades of the first arrivals. This model has been constructed from evidence mostly from southern and eastern regions of New Zealand, but a more complicated pattern may apply in the more humid western and northern regions where forests are more resilient to burning. We present a new pollen record from Lake Pupuke, Auckland, northern New Zealand, that charts the changing vegetation cover over the last 1000 years, before and after the arrival of people. Previous results from this site concurred with the rapid transformation model, although sampling resolution, chronology and sediment disturbance make that interpretation equivocal. Our new record is dated principally by tephrochronology together with radiocarbon dating, and includes a cryptotephra deposit identified as Kaharoa tephra, a key marker for first settlement in northern New Zealand. Its discovery and stratigraphic position below two Rangitoto-derived tephras enables a clearer picture of environmental change to be drawn. The new pollen record shows an early phase (step 1) of minor, localised forest clearance around the time of Kaharoa tephra (c. 1314 AD) followed by a later, more extensive deforestation phase (step 2) commencing at around the time of deposition of the Rangitoto tephras (c. 1400‒1450 AD). This pattern, which needs to be corroborated from other well-resolved records from northern New Zealand, concurs with an emerging hypothesis that the ‘Little Ice Age’ had a significant impact on pre-European Māori with the onset of harsher conditions causing a consolidation of populations and later environmental impact in northern New Zealand.

year: 2018