ORCID Profile
0000-0001-5995-2602
Current Organisation
University of Queensland
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Microbial Ecology | Microbiology | Genomics | Bioinformatics | Wastewater treatment processes | Phylogeny and Comparative Analysis | Chemical engineering | Conservation and Biodiversity | Industrial microbiology (incl. biofeedstocks) | Environmental biotechnology not elsewhere classified |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Climate and Climate Change not elsewhere classified | Expanding Knowledge in the Earth Sciences | Flora, Fauna and Biodiversity at Regional or Larger Scales
Related Links
Publications
Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi
Publisher: Springer Science and Business Media LLC
Date: 16-01-2019
Phylogenetic diversity of archaea and bacteria in the anoxic zone of a meromictic lake (Lake Pavin, France)
Publisher: American Society for Microbiology
Date: 15-03-2007
DOI: 10.1128/AEM.01490-06
Abstract: The compositions of archaeal and bacterial populations at different depths (60 m [mixolimnion-chemocline interface], 70 m [chemocline-subchemocline interface], 90 m, and 92 m [the water-sediment interface]) in the anoxic zone of the water column in Lake Pavin, a freshwater permanently stratified mountain lake in France, were determined. Phylogenetic trees were constructed from sequences to assess archaeal and bacterial ersity at the four sites.
Recoding enhances the metabolic capabilities of two novel methylotrophic Asgardarchaeota lineages
Publisher: Cold Spring Harbor Laboratory
Date: 19-02-2021
DOI: 10.1101/2021.02.19.431964
Abstract: Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative organoheterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including deep subsurface, shallow lake, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four novel lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Hodarchaeia class nov. and Cand. Jordarchaeia class nov., derived from the gods Hod and Jord in Norse mythology. Metabolic inference suggests that both novel classes represent methylotrophic acetogens, encoding the transfer of methyl groups, such as methylated amines, to coenzyme M with acetate as the end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e. recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding on the other hand is restricted to Hodarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic lineage with an inferred complete Pyl machinery, likely providing this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of Bacteria and Eukaryotes, in both novel classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.
Evidence for nontraditional mcr -containing archaea contributing to biological methanogenesis in geothermal springs
Publisher: American Association for the Advancement of Science (AAAS)
Date: 28-06-2023
Abstract: Recent discoveries of methyl-coenzyme M reductase–encoding genes ( mcr ) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on 13 C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr -containing archaea inhabiting the springs genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting erse nontraditional mcr -containing archaea as previously unrecognized methane sources.
Molecular diversity of the foregut bacteria community in the dromedary camel (Camelus dromedarius)
Publisher: Wiley
Date: 14-09-2011
DOI: 10.1111/J.1462-2920.2011.02579.X
Abstract: The molecular ersity of the foregut bacterial community in the dromedary camel (Camelus dromedarius) in Central Australia was investigated through comparative analyses of 16S rRNA gene sequences prepared from the foregut contents of 12 adult feral camels fed on native vegetation. A total of 267 full-length 16S rRNA gene clones were examined, with 151 operational taxonomic units (OTUs) identified at a 99% species-level identity cut-off criterion. The prediction of actual ersity in the foregut of the dromedary camel using the Chaol approach was 238 OTUs, while the richness and evenness of the ersity estimated using Shannon index was 4.84. The majority of bacteria in the current study were affiliated with the bacterial phylum Firmicutes (67% of total clones) and were related to the classes Clostridia, Bacilli and Mollicutes, followed by the Bacteroidetes (25%) that were mostly represented by the family Prevotellaceae. The remaining phyla were represented by Actinobacteria, Chloroflexi, Cynophyta, Lentisphaerae, Planctomycetes, Proteobacteria and Sphirochaetes. Moreover, 11 clones of cultivated bacteria were identified as Brevundimonas sp., Butyrivibrio fibrisolvens, Prevotella sp. and Ruminococcus flavefaciens. The novelty in this foregut environment is remarkable where 97% of the OTUs were distantly related to any known sequence in the public database.
Methanotrophy across a natural permafrost thaw environment
Publisher: Springer Science and Business Media LLC
Date: 28-06-2018
The effect of methane and odd-chain fatty acids on 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV) synthesis by a Methylosinus-dominated mixed culture
Publisher: Springer Science and Business Media LLC
Date: 12-2019
DOI: 10.1186/S40643-019-0285-1
Abstract: A methanotrophic community was enriched in a semi-continuous reactor under non-aseptic conditions with methane and ammonia as carbon and nitrogen source. After a year of operation, Methylosinus sp., accounted for 80% relative abundance of the total sequences identified from potential polyhydroxyalkanoates (PHAs) producers, dominated the methane-fed enrichment. Prior to induction of PHA accumulation, cells harvested from the parent reactor contained low level of PHA at 4.0 ± 0.3 wt%. The cells were later incubated in the absence of ammonia with various combinations of methane, propionic acid, and valeric acid to induce biosynthesis of poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate- co -3-hydroxyvalerate) (PHBV). Previous studies reported that methanotrophic utilization of odd-chain fatty acids for the production of PHAs requires reducing power from methane oxidation. However, our findings demonstrated that the PHB-containing methanotrophic enrichment does not require methane availability to generate 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV)—when odd-chain fatty acids are presented. The enrichment yielded up to 14 wt% PHA with various mole fractions of 3HV monomer depending on the availability of methane and odd-fatty acids. Overall, the addition of valeric acid resulted in a higher PHA content and a higher 3HV fraction. The highest 3HV fraction (up to 65 mol%) was obtained from the methane–valeric acid experiment, which is higher than those previously reported for PHA-producing methanotrophic mixed microbial cultures.
The effect of coal rank on biogenic methane potential and microbial composition
Publisher: Elsevier BV
Date: 2016
Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea.
Publisher: Springer Science and Business Media LLC
Date: 08-10-2019
DOI: 10.1038/S41467-019-12574-Y
Abstract: Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) ergent to existing archaeal lineages. Here, we study the mcr -containing archaeal MAGs from several hot springs, which reveal further expansion in the ersity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr -containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.
Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira
Publisher: Springer Science and Business Media LLC
Date: 17-04-2023
DOI: 10.1038/S41396-023-01409-W
Abstract: The recent discovery of Nitrospira species capable of complete ammonia oxidation (comammox) in non-marine natural and engineered ecosystems under mesothermal conditions has changed our understanding of microbial nitrification. However, little is known about the occurrence of comammox bacteria or their ability to survive in moderately thermal and/or hyperthermal habitats. Here, we report the wide distribution of comammox Nitrospira in five terrestrial hot springs at temperatures ranging from 36 to 80°C and provide metagenome-assembled genomes of 11 new comammox strains. Interestingly, the identification of dissimilatory nitrate reduction to ammonium (DNRA) in thermophilic comammox Nitrospira lineages suggests that they have versatile ecological functions as both sinks and sources of ammonia, in contrast to the described mesophilic comammox lineages, which lack the DNRA pathway. Furthermore, the in situ expression of key genes associated with nitrogen metabolism, thermal adaptation, and oxidative stress confirmed their ability to survive in the studied hot springs and their contribution to nitrification in these environments. Additionally, the smaller genome size and higher GC content, less polar and more charged amino acids in usage profiles, and the expression of a large number of heat shock proteins compared to mesophilic comammox strains presumably confer tolerance to thermal stress. These novel insights into the occurrence, metabolic activity, and adaptation of comammox Nitrospira in thermal habitats further expand our understanding of the global distribution of comammox Nitrospira and have significant implications for how these unique microorganisms have evolved thermal tolerance strategies.
Differences down-under: Alcohol-fueled methanogenesis by archaea present in Australian macropodids
Publisher: Springer Science and Business Media LLC
Date: 29-03-2016
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Publisher: Springer Science and Business Media LLC
Date: 11-09-2017
DOI: 10.1038/S41564-017-0012-7
Abstract: Challenges in cultivating microorganisms have limited the phylogenetic ersity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from ,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic ersity of bacterial and archaeal genome trees by % and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative ersity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.
Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages
Publisher: Springer Science and Business Media LLC
Date: 28-06-2021
DOI: 10.1038/S43705-021-00032-0
Abstract: Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca . Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero-organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of bacteria and eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.
Genome-centric analysis of microbial populations enriched by hydraulic fracture fluid additives in a coal bed methane production well
Publisher: Frontiers Media SA
Date: 08-06-2016
Chloroform decreases rumen methanogenesis and methanogen populations without altering rumen function in cattle
Publisher: Elsevier BV
Date: 06-2011
Draft genome sequence of Treponema sp. strain JC4, a novel spirochete isolated from the bovine rumen
Publisher: American Society for Microbiology
Date: 08-2012
DOI: 10.1128/JB.00754-12
Abstract: Morphologically and biochemically erse members of the Treponema genus are present in the gastrointestinal tract of ruminants, yet very little is understood about their functional importance to this microbiome. Here we describe the annotated draft genome sequence of Treponema sp. strain JC4, a novel spirochete isolated from a bovine rumen s le.
Identification of metabolically active proteobacterial and archaeal communities in the rumen by DNA- and RNA-derived 16S rRNA gene
Publisher: Oxford University Press (OUP)
Date: 07-2013
DOI: 10.1111/JAM.12270
Abstract: To gain new insights into the metabolic contribution of bacterial group in the rumen. Both DNA- and RNA-derived bacterial 16S ribosomal materials from bovine rumen contents were used as the template for bacterial community and analyse microbiota by three methods namely custom phylogenetic microarray, quantitative real-time PCR and denaturing gradient gel electrophoresis techniques. Bacterial analysis showed that genera affiliating with the Proteobacteria apparently made a greater metabolic contribution to rumen function than their population sizes indicated. Analysis of another rumen microbial group, the methanogens, using clone libraries for the expressed methyl coenzyme reductase subunit A (mcrA) revealed that an uncultivated methanogen clade contributes one-third of RNA-derived mcrA sequences based on a limited number of clones analysed. These uncultivated methanogen species were not observed in the mcrA gene library based on the DNA-derived sequences. The comparison of results obtained from DNA- and RNA-derived materials suggests that some of the Proteobacteria and novel methanogen species appeared to be low in abundance in the rumen maintained on grain-based diets might play a greater role in rumen metabolism. These studies provide the first report to compare high-throughput analysis of bacterial 16S rRNA genes from DNA- and RNA-derived materials to indicate differences that species make to community structure and metabolic activity.
16S rDNA directed PCR primers and detection of methanogens in the bovine rumen
Publisher: Oxford University Press (OUP)
Date: 03-2006
Howardella ureilytica gen. nov., sp. nov., a Gram-positive, coccoid-shaped bacterium from a sheep rumen
Publisher: Microbiology Society
Date: 12-2007
Abstract: An unidentified obligately anaerobic, fastidious, Gram-positive, non-motile, non-spore-forming, non-fermentative coccoid-shaped bacterium (designated strain GPC 589 T ) was isolated from the rumen fluid of a sheep. The major fatty acid constituents ( %) were C 16 : 0 (29.2 %), C 18 : 0 (40.7 %) and an unidentified compound (19.7 %) with an equivalent chain-length of 13.523. The G+C content of the DNA was 34 mol%. The organism was strongly ureolytic and generated ATP through the hydrolysis of urea. Comparative 16S rRNA gene sequence analysis demonstrated that strain GPC 589 T was far removed, phylogenetically, from the ruminococci and related Gram-positive anaerobic cocci but exhibited a phylogenetic association with Clostridium rRNA cluster XIVa [as defined by Collins, M. D., Lawson, P. A., Willems, A., Cordoba, J. J., Fernandez-Garayzabal, J., Garcia, P., Cai, J., Hippe, H. & Farrow, J. A. E. (1994). Int J Syst Bacteriol 44 , 812–826]. Sequence ergence values of 12.5 % or more were observed between strain GPC 589 T and all other recognized species within this and related rRNA clostridial clusters. Phylogenetic analysis showed that strain GPC 589 T represents a new genus within cluster XIVa. On the basis of both phylogenetic and phenotypic evidence, it is proposed that strain GPC 589 T should be classified as representing a new genus and novel species, Howardella ureilytica gen. nov., sp. nov. The type strain is strain GPC 589 T (=DSM 15118 T =JCM 13267 T ).
Correction: Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota
Publisher: Springer Science and Business Media LLC
Date: 24-01-2022
Community composition and density of Methanogens in the foregut of the Tammar Wallaby (Macropus eugenii)
Publisher: American Society for Microbiology
Date: 15-04-2009
DOI: 10.1128/AEM.02436-08
Abstract: The composition of the methanogenic archaeal community in the foregut contents of Tammar wallabies ( Macropus eugenii ) was studied using 16S rRNA and methyl coenzyme reductase subunit A ( mcrA ) gene clone libraries. Methanogens belonging to the Methanobacteriales and a well-supported cluster of uncultivated archaeon sequences previously observed in the ovine and bovine rumens were found. Methanogen densities ranged from 7.0 × 10 5 and 3.9 × 10 6 cells per gram of wet weight.
Evidence for non‐methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales
Publisher: Wiley
Date: 18-06-2020
Abstract: Recent discoveries of mcr and mcr ‐like genes in genomes from erse archaeal lineages suggest that methane metabolism is an ancient pathway with a complicated evolutionary history. One conventional view is that methanogenesis is an ancestral metabolism of the class Thermoplasmata . Through comparative genomic analysis of 12 Thermoplasmata metagenome‐assembled genomes (MAGs) basal to the Methanomassiliicoccales , we show that these microorganisms do not encode the genes required for methanogenesis. Further analysis of 770 Ca . Thermoplasmatota genomes/MAGs found no evidence of mcrA homologues outside of the Methanomassiliicoccales . Together, these results suggest that methanogenesis was laterally acquired by an ancestor of the Methanomassiliicoccales . The 12 analysed MAGs include representatives from four orders basal to the Methanomassiliicoccales , including a high‐quality MAG that likely represents a new order, Ca . Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use erse energy conservation pathways, including heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two lineages are widespread among anoxic, sedimentary environments, whereas Ca . Lunaplasma lacustris has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide insight into the evolutionary history of methanogenesis within the Ca . Thermoplasmatota.
Genome-centric view of carbon processing in thawing permafrost
Publisher: Springer Science and Business Media LLC
Date: 16-07-2018
DOI: 10.1038/S41586-018-0338-1
Abstract: As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 s les from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the ersity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.
An evolving view of methane metabolism in the Archaea
Publisher: Springer Science and Business Media LLC
Date: 21-01-2019
DOI: 10.1038/S41579-018-0136-7
Abstract: Methane is a key compound in the global carbon cycle that influences both nutrient cycling and the Earth's climate. A limited number of microorganisms control the flux of biologically generated methane, including methane-metabolizing archaea that either produce or consume methane. Methanogenic and methanotrophic archaea belonging to the phylum Euryarchaeota share a genetically similar, interrelated pathway for methane metabolism. The key enzyme in this pathway, the methyl-coenzyme M reductase (Mcr) complex, catalyses the last step in methanogenesis and the first step in methanotrophy. The discovery of mcr and ergent mcr-like genes in new euryarchaeotal lineages and novel archaeal phyla challenges long-held views of the evolutionary origin of this metabolism within the Euryarchaeota. Divergent mcr-like genes have recently been shown to oxidize short-chain alkanes, indicating that these complexes have evolved to metabolize substrates other than methane. In this Review, we examine the ersity, metabolism and evolutionary history of mcr-containing archaea in light of these recent discoveries.
Genome sequence of Staphylococcus epidermidis strain AU12-03, isolated from an intravascular catheter
Publisher: American Society for Microbiology
Date: 12-2012
DOI: 10.1128/JB.01693-12
Abstract: In recent years, Staphylococcus epidermidis has become a major nosocomial pathogen and the most common cause of intravascular catheter-related bacteremia, which can increase morbidity and mortality and significantly affect patient recovery. We report a draft genome sequence of Staphylococcus epidermidis AU12-03, isolated from an intravascular catheter tip.
Thermophilic production of poly(3-hydroxybutyrate-co-3-hydrovalerate) by a mixed methane-utilizing culture
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.NBT.2019.06.008
Abstract: The production of polyhydroxyalkanoates (PHAs) from methane is limited to mesophiles and thus suffers from high energy requirements for cooling. To address this issue, the use of thermophilic processes is gaining interest, as this strategy may deliver improved economic feasibility for PHA production. This study reports the first thermophilic PHA-producing culture grown on methane at 55 °C in fill-and-draw batch reactors. Harvested cells were incubated with various combinations of methane, propionic acid and valeric acid to assess their capacity for the synthesis of poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). Only PHB was produced when fed with methane alone. The addition of odd-carbon-number fatty acids resulted in higher PHA content with 3 HV fractions in the range of 15-99 mol%, depending on the types of fatty acids added. Acetic acid addition enhanced the synthesis of 3HB monomer, but not of 3 HV. On increasing the temperature to 58 °C, PHA productivity was not significantly affected.
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-10-2015
Abstract: The production and consumption of methane by microorganisms play a major role in the global carbon cycle. Although these processes can occur in a range of environments, from animal guts to the deep ocean, these metabolisms are confined to the Archaea. Evans et al. used metagenomics to assemble two nearly complete archaeal genomes from deep groundwater methanogens (see the Perspective by Lloyd). The two reconstructed genomes are members of the recently described Bathyarchaeota and not the phylum to which all previously known methane-metabolizing archaea belonged. Science , this issue p. 434 , see also p. 384
The influence of hydrogeological disturbance and mining on coal seam microbial communities
Publisher: Wiley
Date: 06-11-2016
DOI: 10.1111/GBI.12166
Abstract: The microbial communities present in two underground coal mines in the Bowen Basin, Queensland, Australia, were investigated to deduce the effect of pumping and mining on subsurface methanogens and methanotrophs. The micro-organisms in pumped water from the actively mined areas, as well as, pre- and post-mining formation waters were analyzed using 16S rRNA gene licon sequencing. The methane stable isotope composition of Bowen Basin coal seam indicates that methanogenesis has occurred in the geological past. More recently at the mine site, changing groundwater flow dynamics and the introduction of oxygen in the subsurface has increased microbial biomass and ersity. Consistent with microbial communities found in other coal seam environments, pumped coal mine waters from the subsurface were dominated by bacteria belonging to the genera Pseudomonas and the family Rhodocyclaceae. These environments and bacterial communities supported a methanogen population, including Methanobacteriaceae, Methanococcaceae and Methanosaeta. However, one of the most ubiquitous micro-organisms in anoxic coal mine waters belonged to the family 'Candidatus Methanoperedenaceae'. As the Archaeal family 'Candidatus Methanoperedenaceae' has not been extensively defined, the one studied species in the family is capable of anaerobic methane oxidation coupled to nitrate reduction. This introduces the possibility that a methane cycle between archaeal methanogenesis and methanotrophy may exist in the anoxic waters of the coal seam after hydrogeological disturbance.
Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota
Publisher: Springer Science and Business Media LLC
Date: 18-06-2018
DOI: 10.1038/NMICROBIOL.2016.170
Abstract: Methanogenesis is the primary biogenic source of methane in the atmosphere and a key contributor to climate change. The long-standing dogma that methanogenesis originated within the Euryarchaeota was recently challenged by the discovery of putative methane-metabolizing genes in members of the Bathyarchaeota, suggesting that methanogenesis may be more phylogenetically widespread than currently appreciated. Here, we present the discovery of ergent methyl-coenzyme M reductase genes in population genomes recovered from anoxic environments with high methane flux that belong to a new archaeal phylum, the Verstraetearchaeota. These archaea encode the genes required for methylotrophic methanogenesis, and may conserve energy using a mechanism similar to that proposed for the obligate H 2 -dependent methylotrophic Methanomassiliicoccales and recently described Candidatus ‘Methanofastidiosa’. Our findings indicate that we are only beginning to understand methanogen ersity and support an ancient origin for methane metabolism in the Archaea, which is changing our understanding of the global carbon cycle.
16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs
Publisher: Elsevier BV
Date: 10-2004
DOI: 10.1016/J.ANAEROBE.2004.05.003
Abstract: The population densities and identities of methanogens colonising new-born lambs in a grazing flock were determined from rumen s les collected at regular intervals after birth. Methanogen colonisation was found at the first s ling (1-3 days after birth) and population densities reached around 10(4) methanogens per gram at 1 week of age. Population densities increased in an exponential manner to a maximum of 10(8)-10(9) per gram at 3 weeks of age. To identify methanogens, PCR primers specific for each of the Archaea a grouping of the orders Methanomicrobiales, Methanosarcinales and Methanococcales the order Methanobacteriales the order Methanococcales the order Methanosarcinales the genus Methanobacterium and the genus Methanobrevibacter were designed. Primer-pair specificities were confirmed in tests with target and non-target micro-organisms. PCR analysis of DNA extracts revealed that all the detectable ruminal methanogens belonged to the order Methanobacteriales, with no methanogens belonging to the Methanomicrobiales, the Methanosarcinales, or the Methanococcales being detected. In 3 lambs, the initial colonising methanogens were Methanobrevibacter spp. and in 2 lambs were a mixture of Methanobrevibacter and Methanobacterium spp. In the latter case, the initial colonising Methanobacterium spp. subsequently disappeared and were not detectable 12-19 days after birth. Seven weeks after birth, lambs contained only Methanobrevibacter spp. This study, the first to provide information on the identities of methanogens colonising pre-ruminants, suggests that the predominant methanogens found in the mature rumen establish very soon after birth and well before a functioning rumen develops.
Genome sequence of Stenotrophomonas maltophilia strain AU12-09, isolated from an intravascular catheter
Publisher: American Society for Microbiology
Date: 27-06-2013
Abstract: Stenotrophomonas maltophilia is an opportunistic nosocomial pathogen that is characterized by its high-level intrinsic resistance to a variety of antibiotics and its ability to form biofilms. Here, we report the draft genome sequence of Stenotrophomonas maltophilia AU12-09, isolated from an intravascular catheter tip.
Temporal changes in microbial community composition during culture enrichment experiments with Indonesian coals
Publisher: Elsevier BV
Date: 2015
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