Paul N. Evans's research while affiliated with The University of Queensland and other places

Publications (33)

Article
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Candidatus Bathyarchaeia" is a phylogenetically diverse and widely distributed lineage often in high abundance in anoxic submarine sediments; however, their evolution and ecological roles in terrestrial geothermal habitats are poorly understood. In the present study, 35 Ca. Bathyarchaeia metagenome-assembled genomes (MAGs) were recovered from hot s...
Article
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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...
Preprint
Full-text available
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. Her...
Article
Recent discoveries of mcr and mcr-like genes in genomes from diverse 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 metagenom...
Article
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Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/ ), a de novo developed data management and exploration platform, as a s...
Preprint
Recent discoveries of mcr and mcr-like complexes in genomes from diverse archaeal lineages suggest that methane (and more broadly alkane) metabolism is an ancient pathway with complicated evolutionary histories. The conventional view is that methanogenesis is an ancestral metabolism of the archaeal class Thermoplasmata. Through comparative genomic...
Article
Full-text available
Together these results show that hot spring environments harbor many mcr-containing organisms from outside of the Euryarchaeota and further expand the diversity of Mcr meditated methane or alkane metabolism processes. The predicted wide range of metabolic mechanisms suggests that these organisms may utilize diverse and as yet unidentified substrate...
Article
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 Eury...
Article
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The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane and potentially propane. The number of archaeal clades encoding the MCR complex continues to grow, suggesting that this complex was inh...
Preprint
The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane and potentially propane. The number of archaeal clades encoding the MCR complex continues to grow, suggesting that this complex was inh...
Article
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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 samples from a permafrost thaw gradient to reco...
Article
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The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotr...
Preprint
The recent discovery of key methane-metabolizing genes in the genomes from the archaeal phyla Bathyarchaeota and Verstraetearchaeota has expanded our understanding of the distribution of methane metabolism outside of the phylum Euryarchaeota. Here, we recovered two near-complete crenarchaeotal metagenome-assembled genomes (MAGs) from circumneutral...
Article
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In the original version of this Article, the authors stated that the archaeal phylum Parvarchaeota was previously represented by only two single-cell genomes (ARMAN-4_'5-way FS' and ARMAN-5_'5-way FS'). However, these are in fact unpublished, low-quality metagenome-assembled genomes (MAGs) obtained from Richmond Mine, California. In addition, the a...
Article
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Challenges in cultivating microorganisms have limited the phylogenetic diversity 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 an...
Article
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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 mo...
Article
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Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are c...
Article
The Australian macropodids (kangaroos and wallabies) possess a distinctive foregut microbiota that contributes to their reduced methane emissions. However, methanogenic archaea are present within the macropodid foregut, although there is scant understanding of these microbes. Here, an isolate taxonomically assigned to the Methanosphaera genus (Meth...
Article
Demand for natural gas is expected to increase faster than any other fossil fuel over the coming decades. Australian coal bed methane (CBM) resources are among the largest in the world and are already utilized to meet increasing demand. The majority of methane contained within CBM producing coal beds is microbially generated and low rank coals are...
Article
Methanogenic and methanotrophic archaea play important roles in the global flux of methane. Culture-independent approaches are providing deeper insight into the diversity and evolution of methane-metabolizing microorganisms, but, until now, no compelling evidence has existed for methane metabolism in archaea outside the phylum Euryarchaeota. We per...
Article
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http://microbiology.publish.csiro.au/paper/MA15003.htm Methanogenic archaea resident in the mammalian gastrointestinal tract have long been recognised for their capacity to participate in interspecies hydrogen transfer, with commensurate positive effects on plant biomass conversion. However, there is also still much to learn about these methanogen...
Article
Temporal changes in microbial community structures during methanogenesis were investigated in cultures of South Sumatra Basin (SSB) coalbed methane (CBM) formation water (SSB5) grown on three coals of different rank (Burung sub bituminous Rv 0.39%, Mangus sub bituminous Rv 0.5%, Mangus anthracite Rv 2.2%). Methane production accelerated from day 6,...
Article
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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 gradie...
Article
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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.
Article
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 cathe...
Article
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Morphologically and biochemically diverse 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 sample.
Article
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The molecular diversity 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, wit...
Article
Full-text available
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 t...

Citations

... Helarchaeota species encodes the complete set of enzymes allowing these archaea to perform methanogenesis or alkanotrophy under some conditions. [86][87][88][89]91 The alkane oxidation would rely on an association with sulfate-reducing bacteria. 92 In the mentioned methanogens and alkanotrophs, the alkane chemistry is supposed to be performed by ACRs. ...
... Recent studies have uncovered archaeal lineages, recovered from Frontiers in Microbiology 02 frontiersin.org geothermal springs and deep-sea sediments, which possess more than one of these diverse genetic code systems (Mukai et al., 2017;Sun et al., 2021). Here, we discuss the structural elements, regulatory mechanisms, and biosynthetic strategies associated with these systems. ...
... If methanogenesis was the metabolism present in the last common ancestor of these lineages, Culexarchaeia will aid in understanding shifts from methanogenic to non-methanogenic lifestyles in the TACK archaea. This type of transition is considered to have been an important process in archaeal evolution and is partially responsible for the observed patchwork distribution of MCRencoding lineages [15,94,95]. We expect that as more deeply branching lineages in the TACK superphylum are recovered, this will help resolve the complicated history of these metabolic transitions and further our understanding of the metabolic capabilities encoded by this diverse superphylum. ...
... Recent estimates show substantial winter C loss [9], which may be greater than the average growing season C uptake [10]. While the winter months include large air temperature fluctuations and extreme temperature minimums [11], the temperatures found in much of the soil profile of permafrost or seasonally frozen bogs can remain stable and just below the freezing point (−1 to −5°C) [5,12,13]. Bacteria have been shown to remain active below the freezing point in soils with both catabolic and anabolic activities observed [14][15][16]. Activity is likely facilitated by a portion of the water remaining liquid at temperatures below 0°C with evidence that more than 20% of the water can remain unfrozen in peat soils incubated between −1 and −5°C [17]. ...
... Bins produced from each program were refined with DAS_Tool [24]. In addition, the published MAG JZ-Bin-30, recovered from a metagenome obtained from a geothermal well in the Yunnan province (China) [25,26], was downloaded from the IMG/M portal. CheckM [27] was used to estimate MAG completeness, redundancy, and relative abundance. ...
... If methanogenesis was the metabolism present in the last common ancestor of these lineages, Culexarchaeia will aid in understanding shifts from methanogenic to non-methanogenic lifestyles in the TACK archaea. This type of transition is considered to have been an important process in archaeal evolution and is partially responsible for the observed patchwork distribution of MCRencoding lineages [15,94,95]. We expect that as more deeply branching lineages in the TACK superphylum are recovered, this will help resolve the complicated history of these metabolic transitions and further our understanding of the metabolic capabilities encoded by this diverse superphylum. ...
... Interestingly, we recovered mcr subunits in lineages that are not considered as canonical methanogenic lineages [38]. These include two genomes of Bathyarchaeota related to BA1 and BA2 (GCA_002509245.1 and GCA_001399805.1) [39], and one Archaeoglobi genome related to JdFR-42 (GCA_002010305) [40,41]. These genomes have been described as having divergent MCR genes. ...
... In order to verify this so-far undescribed and surprising observation, the authors had to compare their data with other publicly available datasets from the same ecosystem but geographically distant sites. Their data were compared with previously established culture collections from Germany and Norway [32,31] as well as with Austrian and Swedish metagenomes [8,7,27,29,57]. This comparative study confirmed the initial hypothesis of naturally occurring antimicrobial resistances in pristine environments and facilitated the development of a new theory about resistome development in natural habitats. ...
... This way CO2 is removed from the atmosphere and stored in the ocean floors (Broines et al., 2004). Chemolithoautotrophic archaea and bacteria fix CO2 in deep water zones with no light penetration (Muller et al., 2018) and at the surface during polar winter (Singleton et al., 2018) thus, contributing to surface ocean respiration ad cycling of elements. sea floor methanogens and methanotrophs are important consumers and producers of CH4 but their influence on atmospheric flux of CH4 is uncertain (Emerson et al., 2018). ...
... Accordingly, all the assembled genomes have at least 50% completeness, and nearly half of the total MAGs are ≥90% complete with less than 5% contamination. In a separate study, MAG analyses of two archaea from a hyperthermal hot spring identified unrecognized methane-metabolising sequences outside of the phylum Euryarchaeota [94]. In another work, Kadnikov et al. [95] recovered a complete genome of the candidate phylum BRC1 using MAG analysis of a deep subsurface thermal aquifer. ...