Publications by authors named "Ben J Woodcroft"

32 Publications

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years.

Microbiome 2021 10 6;9(1):199. Epub 2021 Oct 6.

Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China.

Background: Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically diverse assemblages can be and what causes them to transition between states remains poorly understood. We studied monthly activated sludge (AS) samples collected over 9 years from a full-scale wastewater treatment plant to answer how complex AS communities evolve in the long term and how the community functions change when there is a disturbance in operational parameters.

Results: Here, we show that a microbial community in activated sludge (AS) system fluctuated around a stable average for 3 years but was then abruptly pushed into an alternative stable state by a simple transient disturbance (bleaching). While the taxonomic composition rapidly turned into a new state following the disturbance, the metabolic profile of the community and system performance remained remarkably stable. A total of 920 metagenome-assembled genomes (MAGs), representing approximately 70% of the community in the studied AS ecosystem, were recovered from the 97 monthly AS metagenomes. Comparative genomic analysis revealed an increased ability to aggregate in the cohorts of MAGs with correlated dynamics that are dominant after the bleaching event. Fine-scale analysis of dynamics also revealed cohorts that dominated during different periods and showed successional dynamics on seasonal and longer time scales due to temperature fluctuation and gradual changes in mean residence time in the reactor, respectively.

Conclusions: Our work highlights that communities can assume different stable states under highly similar environmental conditions and that a specific disturbance threshold may lead to a rapid shift in community composition. Video Abstract.
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http://dx.doi.org/10.1186/s40168-021-01151-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8495973PMC
October 2021

Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes.

Nat Commun 2021 10 5;12(1):5815. Epub 2021 Oct 5.

Department of Microbiology, The Ohio State University, 496W 12th Ave, Columbus, OH, 43210, USA.

Northern post-glacial lakes are significant, increasing sources of atmospheric carbon through ebullition (bubbling) of microbially-produced methane (CH) from sediments. Ebullitive CH flux correlates strongly with temperature, reflecting that solar radiation drives emissions. However, here we show that the slope of the temperature-CH flux relationship differs spatially across two post-glacial lakes in Sweden. We compared these CH emission patterns with sediment microbial (metagenomic and amplicon), isotopic, and geochemical data. The temperature-associated increase in CH emissions was greater in lake middles-where methanogens were more abundant-than edges, and sediment communities were distinct between edges and middles. Microbial abundances, including those of CH-cycling microorganisms and syntrophs, were predictive of porewater CH concentrations. Results suggest that deeper lake regions, which currently emit less CH than shallower edges, could add substantially to CH emissions in a warmer Arctic and that CH emission predictions may be improved by accounting for spatial variations in sediment microbiota.
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http://dx.doi.org/10.1038/s41467-021-25983-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8492752PMC
October 2021

Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases.

Mol Biol Evol 2019 12;36(12):2922-2924

School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.

Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers.
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http://dx.doi.org/10.1093/molbev/msz185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6878946PMC
December 2019

An evolving view of methane metabolism in the Archaea.

Nat Rev Microbiol 2019 04 21;17(4):219-232. Epub 2019 Jan 21.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia.

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 divergent 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 diversity, metabolism and evolutionary history of mcr-containing archaea in light of these recent discoveries.
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http://dx.doi.org/10.1038/s41579-018-0136-7DOI Listing
April 2019

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi.

ISME J 2019 05 16;13(5):1269-1279. Epub 2019 Jan 16.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.

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 continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; Ca. Polytropus marinifundus gen. nov. sp. nov.) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Ca. Bathyarchaeota and Ca. Syntrophoarchaeum MAGs. Ca. P. marinifundus is basal to members of the class Archaeoglobi, and encodes the genes for β-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. Ca. P. marinifundus also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. Phylogenetic analysis suggests that the Ca. P. marinifundus MCR operons were horizontally transferred, changing our understanding of the evolution and distribution of this complex in the Archaea.
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http://dx.doi.org/10.1038/s41396-018-0343-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474303PMC
May 2019

Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov.

Syst Appl Microbiol 2019 Jan 14;42(1):54-66. Epub 2018 Dec 14.

Department of Microbiology, The Ohio State University, Columbus, OH 43210, United States; Department of Soil, Water and Environmental Sciences, University of Arizona, Tucson, AZ 85716, United States. Electronic address:

The phylum Caldiserica was identified from the hot spring 16S rRNA gene lineage 'OP5' and named for the sole isolate Caldisericum exile, a hot spring sulfur-reducing chemoheterotroph. Here we characterize 7 Caldiserica metagenome-assembled genomes (MAGs) from a thawing permafrost site in Stordalen Mire, Arctic Sweden. By 16S rRNA and marker gene phylogenies, and average nucleotide and amino acid identities, these Stordalen Mire Caldiserica (SMC) MAGs form part of a divergent clade from C. exile. Genome and meta-transcriptome and proteome analyses suggest that unlike Caldisericum, the SMCs (i) are carbohydrate- and possibly amino acid fermenters that can use labile plant compounds and peptides, and (ii) encode adaptations to low temperature. The SMC clade rose to community dominance within permafrost, with a peak metagenome-based relative abundance of ∼60%. It was also physiologically active in the upper seasonally-thawed soil. Beyond Stordalen Mire, analysis of 16S rRNA gene surveys indicated a global distribution of this clade, predominantly in anaerobic, carbon-rich and cold environments. These findings establish the SMCs as four novel phenotypically and ecologically distinct species within a single novel genus, distinct from C. exile clade at the phylum level. The SMCs are thus part of a novel cold-habitat phylum for an understudied, globally-distributed superphylum encompassing the Caldiserica. We propose the names Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., Ca. Cryosericum gen. nov., Ca. Cryosericum septentrionale sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., and Ca. C. terrychapinii sp. nov.
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http://dx.doi.org/10.1016/j.syapm.2018.12.003DOI Listing
January 2019

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.

mSystems 2018 Sep-Oct;3(5). Epub 2018 Oct 2.

Department of Microbiology, The Ohio State University, Columbus, Ohio, USA.

Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire field site in northern Sweden. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts (), implicating viruses in infecting abundant microbial lineages from , , and , including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic. This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870-880, 2018, https://doi.org/10.1038/s41564-018-0190-y). We compared the ecology of the recovered vOTUs along a permafrost thaw gradient and found (i) habitat specificity, (ii) a shift in viral community identity from soil-like to aquatic-like viruses, (iii) infection of dominant microbial hosts, and (iv) carriage of host metabolic genes. These vOTUs can impact ecosystem carbon processing via top-down (inferred from lysing dominant microbial hosts) and bottom-up (inferred from carriage of auxiliary metabolic genes) controls. This work serves as a foundation which future studies can build upon to increase our understanding of the soil virosphere and how viruses affect soil ecosystem services.
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http://dx.doi.org/10.1128/mSystems.00076-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172770PMC
October 2018

Host-linked soil viral ecology along a permafrost thaw gradient.

Nat Microbiol 2018 08 16;3(8):870-880. Epub 2018 Jul 16.

Department of Microbiology, The Ohio State University, Columbus, OH, USA.

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.
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http://dx.doi.org/10.1038/s41564-018-0190-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786970PMC
August 2018

Genome-centric view of carbon processing in thawing permafrost.

Nature 2018 08 16;560(7716):49-54. Epub 2018 Jul 16.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.

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 recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity 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.
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http://dx.doi.org/10.1038/s41586-018-0338-1DOI Listing
August 2018

Methanotrophy across a natural permafrost thaw environment.

ISME J 2018 10 28;12(10):2544-2558. Epub 2018 Jun 28.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia.

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 methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data. Methanotroph community composition and activity varied significantly as thaw progressed from intact permafrost palsa, to partially thawed bog and fully thawed fen. Thirteen methanotroph population genomes were recovered, including two novel genomes belonging to the uncultivated upland soil cluster alpha (USCα) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater δC-CH isotopes and methanotroph abundances showed methane oxidation was greatest below the oxic-anoxic interface in the bog. These results detail the direct effect of thaw on autochthonous methanotroph communities, and their consequent changes in population structure, activity and methane moderation potential.
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http://dx.doi.org/10.1038/s41396-018-0065-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6155033PMC
October 2018

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes.

Nucleic Acids Res 2018 06;46(10):e59

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia.

Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial communities. Gene-centric approaches can be used to gain a comprehensive view of diversity by examining each read independently, but traditional pairwise comparison approaches typically over-classify taxonomy and scale poorly with increasing metagenome and database sizes. Here we introduce GraftM, a tool that uses gene specific packages to rapidly identify gene families in metagenomic data using hidden Markov models (HMMs) or DIAMOND databases, and classifies these sequences using placement into pre-constructed gene trees. The speed and accuracy of GraftM was benchmarked with in silico and in vitro mock communities using taxonomic markers, and was found to have higher accuracy at the family level with a processing time 2.0-3.7× faster than currently available software. Exploration of a wetland metagenome using 16S rRNA- and methyl-coenzyme M reductase (McrA)-specific gpkgs revealed taxonomic and functional shifts across a depth gradient. Analysis of the NCBI nr database using the McrA gpkg allowed the detection of novel sequences belonging to phylum-level lineages. A growing collection of gpkgs is available online (https://github.com/geronimp/graftM_gpkgs), where curated packages can be uploaded and exchanged.
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http://dx.doi.org/10.1093/nar/gky174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007438PMC
June 2018

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Nat Microbiol 2018 Feb;3(2):253

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.

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 authors overlooked two higher-quality published Parvarchaeota MAGs from the same habitat, ARMAN-4 (ADCE00000000) and ARMAN-5 (ADHF00000000) (B. J. Baker et al., Proc. Natl Acad. Sci. USA 107, 8806-8811; 2010). The ARMAN-4 and ARMAN-5 MAGs are estimated to be 68.0% and 76.7% complete with 3.3% and 5.6% contamination, respectively, based on the archaeal-specific marker sets of CheckM. The 11 Parvarchaeota genomes identified in our study were obtained from different Richmond Mine metagenomes, but are highly similar to the ARMAN-4 (ANI of ~99.7%) and ARMAN-5 (ANI of ~99.6%) MAGs. The highest-quality uncultivated bacteria and archaea (UBA) MAGs with similarity to ARMAN-4 and ARMAN-5 are 82.5% and 83.3% complete with 0.9% and 1.9% contamination, respectively. The Parvarchaeota represents only 0.23% of the archaeal genome tree and addition of the ARMAN-4 and ARMAN-5 MAGs do not change the conclusions of this Article, but do impact the phylogenetic gain for this phylum. This has now been corrected in all versions of the Article. An updated version of Fig. 5 has also been used to replace the previous version, with the row for Parvarchaeota removed, and Supplementary Table 15 and Supplementary Table 17 have both been replaced to reflect the availability of the two additional Parvarchaeota genomes. In addition, the Methods incorrectly stated that all metagenomes identified as being from studies where MAGs had previously been recovered were excluded from consideration. Metagenomes from studies where MAGs had previously been recovered were retained if the UBA MAGs provided appreciable improvements in genome quality or phylogenetic diversity. All versions of the Article have been updated to indicate the retention of such metagenomes.
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http://dx.doi.org/10.1038/s41564-017-0083-5DOI Listing
February 2018

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Nat Microbiol 2017 Nov 11;2(11):1533-1542. Epub 2017 Sep 11.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia.

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 and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% 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 diversity 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.
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http://dx.doi.org/10.1038/s41564-017-0012-7DOI Listing
November 2017

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota.

Nat Microbiol 2016 Oct 3;1:16170. Epub 2016 Oct 3.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia.

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 divergent 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-dependent methylotrophic Methanomassiliicoccales and recently described Candidatus 'Methanofastidiosa'. Our findings indicate that we are only beginning to understand methanogen diversity and support an ancient origin for methane metabolism in the Archaea, which is changing our understanding of the global carbon cycle.
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http://dx.doi.org/10.1038/nmicrobiol.2016.170DOI Listing
October 2016

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics.

PeerJ 2016 22;4:e2486. Epub 2016 Sep 22.

Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100-1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036114PMC
http://dx.doi.org/10.7717/peerj.2486DOI Listing
October 2016

The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

PLoS One 2016 14;11(7):e0159128. Epub 2016 Jul 14.

School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia.

In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs) identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the construction of biological materials with diverse morphologies. The SilkSlider predictor software developed here is available at https://github.com/wwood/SilkSlider.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0159128PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4944945PMC
July 2017

OrfM: a fast open reading frame predictor for metagenomic data.

Bioinformatics 2016 09 3;32(17):2702-3. Epub 2016 May 3.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.

Unlabelled: Finding and translating stretches of DNA lacking stop codons is a task common in the analysis of sequence data. However, the computational tools for finding open reading frames are sufficiently slow that they are becoming a bottleneck as the volume of sequence data grows. This computational bottleneck is especially problematic in metagenomics when searching unassembled reads, or screening assembled contigs for genes of interest. Here, we present OrfM, a tool to rapidly identify open reading frames (ORFs) in sequence data by applying the Aho-Corasick algorithm to find regions uninterrupted by stop codons. Benchmarking revealed that OrfM finds identical ORFs to similar tools ('GetOrf' and 'Translate') but is four-five times faster. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers.

Availability And Implementation: Source code and binaries are freely available for download at http://github.com/wwood/OrfM or through GNU Guix under the LGPL 3+ license. OrfM is implemented in C and supported on GNU/Linux and OSX.

Contacts: [email protected]

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btw241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013905PMC
September 2016

Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.

PeerJ 2015 21;3:e968. Epub 2015 May 21.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD , Australia ; Institute for Molecular Bioscience, The University of Queensland , St Lucia, QLD , Australia.

An uncultured non-photosynthetic basal lineage of the Cyanobacteria, the Melainabacteria, was recently characterised by metagenomic analyses of aphotic environmental samples. However, a predatory bacterium, Vampirovibrio chlorellavorus, originally described in 1972 appears to be the first cultured representative of the Melainabacteria based on a 16S rRNA sequence recovered from a lyophilised co-culture of the organism. Here, we sequenced the genome of V. chlorellavorus directly from 36 year-old lyophilised material that could not be resuscitated confirming its identity as a member of the Melainabacteria. We identified attributes in the genome that likely allow V. chlorellavorus to function as an obligate predator of the microalga Chlorella vulgaris, and predict that it is the first described predator to use an Agrobacterium tumefaciens-like conjugative type IV secretion system to invade its host. V. chlorellavorus is the first cyanobacterium recognised to have a predatory lifestyle and further supports the assertion that Melainabacteria are non-photosynthetic.
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http://dx.doi.org/10.7717/peerj.968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451040PMC
June 2015

Methane dynamics regulated by microbial community response to permafrost thaw.

Nature 2014 Oct;514(7523):478-81

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.

Permafrost contains about 50% of the global soil carbon. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ(13)C signature (10-15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus 'Methanoflorens stordalenmirensis' is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.
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http://dx.doi.org/10.1038/nature13798DOI Listing
October 2014

GroopM: an automated tool for the recovery of population genomes from related metagenomes.

PeerJ 2014 30;2:e603. Epub 2014 Sep 30.

Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD , Australia ; Advanced Water Management Center (AWMC), The University of Queensland , St Lucia, QLD , Australia.

Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. We demonstrate the effectiveness of GroopM using synthetic and real-world metagenomes, and show that GroopM produces results comparable with more time consuming, labor-intensive methods.
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http://dx.doi.org/10.7717/peerj.603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183954PMC
October 2014

Discovery of a novel methanogen prevalent in thawing permafrost.

Nat Commun 2014 ;5:3212

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Queensland, Australia.

Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov., belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming.
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http://dx.doi.org/10.1038/ncomms4212DOI Listing
October 2015

Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum.

Genome Biol 2012 Nov 26;13(11):R108. Epub 2012 Nov 26.

Background: The post-genomic era of malaria research provided unprecedented insights into the biology of Plasmodium parasites. Due to the large evolutionary distance to model eukaryotes, however, we lack a profound understanding of many processes in Plasmodium biology. One example is the cell nucleus, which controls the parasite genome in a development- and cell cycle-specific manner through mostly unknown mechanisms. To study this important organelle in detail, we conducted an integrative analysis of the P. falciparum nuclear proteome.

Results: We combined high accuracy mass spectrometry and bioinformatic approaches to present for the first time an experimentally determined core nuclear proteome for P. falciparum. Besides a large number of factors implicated in known nuclear processes, one-third of all detected proteins carry no functional annotation, including many phylum- or genus-specific factors. Importantly, extensive experimental validation using 30 transgenic cell lines confirmed the high specificity of this inventory, and revealed distinct nuclear localization patterns of hitherto uncharacterized proteins. Further, our detailed analysis identified novel protein domains potentially implicated in gene transcription pathways, and sheds important new light on nuclear compartments and processes including regulatory complexes, the nucleolus, nuclear pores, and nuclear import pathways.

Conclusion: Our study provides comprehensive new insight into the biology of the Plasmodium nucleus and will serve as an important platform for dissecting general and parasite-specific nuclear processes in malaria parasites. Moreover, as the first nuclear proteome characterized in any protist organism, it will provide an important resource for studying evolutionary aspects of nuclear biology.
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http://dx.doi.org/10.1186/gb-2012-13-11-r108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053738PMC
November 2012

Determination of protein subcellular localization in apicomplexan parasites.

Trends Parasitol 2012 Dec 17;28(12):546-54. Epub 2012 Sep 17.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Victoria, Australia.

Parasites from the phylum Apicomplexa include causative agents of serious diseases including malaria (Plasmodium spp.) and toxoplasmosis (Toxoplasma gondii). Apicomplexan parasites infect thousands of types of animal cells and send their proteins to an array of compartments within their own cell, as well as exporting proteins into and beyond their host cell. Ascertaining destinations to which individual proteins are delivered allows researchers to better understand parasite biology and to identify potential targets for therapeutic interventions. Our toolkit for establishing subcellular locations of apicomplexan proteins is becoming more extensive and specialized, and here we review developments in this technology.
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http://dx.doi.org/10.1016/j.pt.2012.08.008DOI Listing
December 2012

Marked changes in neuropeptide expression accompany broadcast spawnings in the gastropod Haliotis asinina.

Front Zool 2012 May 9;9(1). Epub 2012 May 9.

Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia.

Introduction: A huge diversity of marine species reproduce by synchronously spawning their gametes into the water column. Although this species-specific event typically occurs in a particular season, the precise time and day of spawning often can not be predicted. There is little understanding of how the environment (e.g. water temperature, day length, tidal and lunar cycle) regulates a population's reproductive physiology to synchronise a spawning event. The Indo-Pacific tropical abalone, Haliotis asinina, has a highly predictable spawning cycle, where individuals release gametes on the evenings of spring high tides on new and full moons during the warmer half of the year. These calculable spawning events uniquely allow for the analysis of the molecular and cellular processes underlying reproduction. Here we characterise neuropeptides produced in H. asinina ganglia that are known in egg-laying molluscs to control vital aspects of reproduction.

Results: We demonstrate that genes encoding APGWamide, myomodulin, the putative proctolin homologue whitnin, FMRFamide, a schistosomin-like peptide (SLP), a molluscan insulin-related peptide (MIP) and a haliotid growth-associated peptide (HGAP) all are differentially expressed in the anterior ganglia during the two week spawning cycle in both male and female abalone. Each gene has a unique and sex-specific expression profile. Despite these differences, expression levels in most of the genes peak at or within 12 h of the spawning event. In contrast, lowest levels of transcript abundance typically occurs 36 h before and 24 h after spawning, with differences in peak and low expression levels being most pronounced in genes orthologous to known molluscan reproduction neuromodulators.

Conclusions: Exploiting the predictable semi-lunar spawning cycle of the gastropod H. asinina, we have identified a suite of evolutionarily-conserved, mollusc-specific and rapidly-evolving neuropeptides that appear to contribute to the regulation of spawning. Dramatic increases and decreases in ganglionic neuropeptide expression levels from 36 h before to 24 h after the broadcast spawning event are consistent with these peptides having a regulatory role in translating environmental signals experienced by a population into a synchronous physiological output, in this case, the release of gametes.
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http://dx.doi.org/10.1186/1742-9994-9-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3434067PMC
May 2012

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

Bioinformatics 2012 Apr 12;28(7):1035-7. Epub 2012 Feb 12.

Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy.

Summary: Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics.

Availability: Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html

Contact: [email protected]
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http://dx.doi.org/10.1093/bioinformatics/bts080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315718PMC
April 2012

The Amphimedon queenslandica genome and the evolution of animal complexity.

Nature 2010 Aug;466(7307):720-6

Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.

Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion and diversification of pan-metazoan transcription factor, signalling pathway and structural genes. This diverse 'toolkit' of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic- and germ-cell specification, cell adhesion, innate immunity and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.
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http://dx.doi.org/10.1038/nature09201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130542PMC
August 2010

Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes.

BMC Genomics 2010 Apr 3;11:222. Epub 2010 Apr 3.

Department of Biochemistry & Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia.

Background: New drug targets are urgently needed for parasites of socio-economic importance. Genes that are essential for parasite survival are highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns are difficult to perform in many species of parasites. We examined the applicability of large-scale essentiality information from four model eukaryotes, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Saccharomyces cerevisiae, to discover essential genes in each of their genomes. Parasite genes that lack orthologues in their host are desirable as selective targets, so we also examined prediction of essential genes within this subset.

Results: Cross-species analyses showed that the evolutionary conservation of genes and the presence of essential orthologues are each strong predictors of essentiality in eukaryotes. Absence of paralogues was also found to be a general predictor of increased relative essentiality. By combining several orthology and essentiality criteria one can select gene sets with up to a five-fold enrichment in essential genes compared with a random selection. We show how quantitative application of such criteria can be used to predict a ranked list of potential drug targets from Ancylostoma caninum and Haemonchus contortus--two blood-feeding strongylid nematodes, for which there are presently limited sequence data but no functional genomic tools.

Conclusions: The present study demonstrates the utility of using orthology information from multiple, diverse eukaryotes to predict essential genes. The data also emphasize the challenge of identifying essential genes among those in a parasite that are absent from its host.
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http://dx.doi.org/10.1186/1471-2164-11-222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867826PMC
April 2010

Automated organelle-based colocalization in whole-cell imaging.

Cytometry A 2009 Nov;75(11):941-50

Institute of Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.

The use of fluorescence microscopy to investigate protein colocalization is an invaluable tool for understanding subcellular structures and their associated proteins. However, current techniques are largely limited to two-dimensional (2D) imaging and often require manual segmentation. Here, we present OBCOL, a methodology to automatically segment and quantify protein colocalization not within an image as a whole but on all individual punctuate organelles within a 3D multichannel image. A wide variety of colocalization statistics may then be calculated on the objects found, and features reported for each such as position, degree of overlap between channels, and number of component objects. OBCOL was validated on imaging of two fluorescent markers (Dextran, EGF) in 3D microscopy imaging. OBCOL's application was then exemplified by investigating the colocalization of three fluorescently tagged proteins (VAMP3, Rab11, and transferrin) on recycling endosomes in mammalian cells. The methodology showed for the first time the diversity of endosomes labeled with one or more of these proteins and quantitatively demonstrated the degree of overlap among these proteins in individual recycling endosomes. The consistent segregation of these markers provides novel evidence for the subcompartmentalization of recycling endosomes. OBCOL is a flexible methodology for 3D multifluorophore image analysis. This study clearly demonstrated its value for investigating subcellular structures and their constituent proteins.
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http://dx.doi.org/10.1002/cyto.a.20786DOI Listing
November 2009

REX1 and Pf62: are they one and the same?

Parasitol Res 2009 Apr;104(5):967-8

Malaria Biology Laboratory, Queensland Institute of Medical Research, Herston, Brisbane, Australia.

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http://dx.doi.org/10.1007/s00436-009-1382-4DOI Listing
April 2009

Widespread transcriptional changes pre-empt the critical pelagic-benthic transition in the vetigastropod Haliotis asinina.

Mol Ecol 2009 Mar 29;18(5):1006-25. Epub 2009 Jan 29.

School of Integrative Biology, The University of Queensland, Saint Lucia Campus, Brisbane, Qld 4072, Australia.

Larval settlement is a vital transition period for marine invertebrates and can have far-reaching effects on the ecology and evolution of a species. To explore the molecular mechanisms of this critical process in a nonmodel organism, the abalone Haliotis asinina, we employed cDNA microarrays. By comparing gene expression profiles through mid- to late larval development and metamorphosis, we identified 144 genes as candidates for a role in competence and/or metamorphosis. Gene characterization indicates ~60% of these are significantly similar to known genes from other taxa, while ~40% are novel. A high 49.3% of genes are gastropod or abalone specific, but none appears to be Lophotrochozoan specific, even though metamorphosis is thought to have had a separate origin in this group. Differentially expressed larval and postlarval genes can be clustered into five categories that reveal strikingly different temporal transcriptional patterns occurring during this phase of development. Some gene activation is contingent upon exogenous cues and correlates with initiation of settlement. Importantly, there is also extensive gene activity associated with the endogenous attainment of competence, which occurs before, and independent of, the exogenous induction of settlement. Our results show that as the haliotid veliger larva matures, it requires coordinated regulation of temporally different batteries of genes involved in a wide range of physiological and developmental processes associated with benthic colonization. Although the signalling pathways operating at metamorphosis may be conserved across the animal kingdom, it appears they regulate the expression of novel genes specific to abalone, gastropods and molluscs during H. asinina metamorphosis.
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http://dx.doi.org/10.1111/j.1365-294X.2008.04078.xDOI Listing
March 2009
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