ORCID Profile
0000-0002-0150-2622
Current Organisations
University of Queensland
,
CSIRO
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Microbial ecology | Wastewater treatment processes | Microbiology | Microbial taxonomy
Publisher: Elsevier BV
Date: 05-2014
DOI: 10.1016/J.WATRES.2014.01.044
Abstract: Anaerobic digestion (AD) is a well-established technology for energy recovery from organic waste streams. Several studies noted that inserting a bioelectrochemical system (BES) inside an anaerobic digester can increase biogas output, however the mechanism behind this was not explored and primary controls were not executed. Here, we evaluated whether a BES could stabilize AD of molasses. Lab-scale digesters were operated in the presence or absence of electrodes, in open (no applied potential) and closed circuit conditions. In the control reactors without electrodes methane production decreased to 50% of the initial rate, while it remained stable in the reactors with electrodes, indicating a stabilizing effect. After 91 days of operation, the now colonized electrodes were introduced in the failing AD reactors to evaluate their remediating capacity. This resulted in an immediate increase in CH4 production and VFA removal. Although a current was generated in the BES operated in closed circuit, no direct effect of applied potential nor current was observed. A high abundance of Methanosaeta was detected on the electrodes, however irrespective of the applied cell potential. This study demonstrated that, in addition to other studies reporting only an increase in methane production, a BES can also remediate AD systems that exhibited process failure. However, the lack of difference between current driven and open circuit systems indicates that the key impact is through biomass retention, rather than electrochemical interaction with the electrodes.
Publisher: American Chemical Society (ACS)
Date: 30-06-2015
DOI: 10.1021/ES506149D
Abstract: The advent of renewable energy conversion systems exacerbates the existing issue of intermittent excess power. Microbial electrosynthesis can use this power to capture CO2 and produce multicarbon compounds as a form of energy storage. As catalysts, microbial populations can be used, provided side reactions such as methanogenesis are avoided. Here a simple but effective approach is presented based on enrichment of a robust microbial community via several culture transfers with H2:CO2 conditions. This culture produced acetate at a concentration of 1.29 ± 0.15 g L(-1) (maximum up to 1.5 g L(-1) 25 mM) from CO2 at a fixed current of -5 Am(-2) in fed-batch bioelectrochemical reactors at high N2:CO2 flow rates. Continuous supply of reducing equivalents enabled acetate production at a rate of 19 ± 2 gm(-2)d(-1) (projected cathode area) in several independent experiments. This is a considerably high rate compared with other unmodified carbon-based cathodes. 58 ± 5% of the electrons was recovered in acetate, whereas 30 ± 10% of the electrons was recovered in H2 as a secondary product. The bioproduction was most likely H2 based however, electrochemical, confocal microscopy, and community analyses of the cathodes suggested the possible involvement of the cathodic biofilm. Together, the enrichment approach and galvanostatic operation enabled instant start-up of the electrosynthesis process and reproducible acetate production profiles.
Publisher: Frontiers Media SA
Date: 18-04-2018
Publisher: Springer Science and Business Media LLC
Date: 07-04-2014
Publisher: American Chemical Society (ACS)
Date: 05-04-2018
Abstract: Free nitrous acid (FNA) exerts a broad range of antimicrobial effects on bacteria, although susceptibility varies considerably among microorganisms. Among nitrifiers found in activated sludge of wastewater treatment processes (WWTPs), nitrite-oxidizing bacteria (NOB) are more susceptible to FNA compared to ammonia-oxidizing bacteria (AOB). This selective inhibition of NOB over AOB in WWTPs bypasses nitrate production and improves the efficiency and costs of the nitrogen removal process in both the activated sludge and anaerobic ammonium oxidation (Anammox) system. However, the molecular mechanisms governing this atypical tolerance of AOB to FNA have yet to be understood. Herein we investigate the varying effects of the antimicrobial FNA on activated sludge containing AOB and NOB using an integrated metagenomics and label-free quantitative sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) metaproteomic approach. The Nitrosomonas genus of AOB, on exposure to FNA, maintains internal homeostasis by upregulating a number of known oxidative stress enzymes, such as pteridine reductase and dihydrolipoyl dehydrogenase. Denitrifying enzymes were upregulated on exposure to FNA, suggesting the detoxification of nitrite to nitric oxide. Interestingly, proteins involved in stress response mechanisms, such as DNA and protein repair enzymes, phage prevention proteins, and iron transport proteins, were upregulated on exposure to FNA. In addition enzymes involved in energy generation were also upregulated on exposure to FNA. The total proteins specifically derived from the NOB genus Nitrobacter was low and, as such, did not allow for the elucidation of the response mechanism to FNA exposure. These findings give us an understanding of the adaptive mechanisms of tolerance within the AOB Nitrosomonas to the biocidal agent FNA.
Publisher: Wiley
Date: 22-07-2016
Abstract: Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across erse environments provide the key to understanding the phylogenetic and metabolic ersity of these interactive communities.
Publisher: Elsevier BV
Date: 04-2020
Publisher: Springer Science and Business Media LLC
Date: 12-2017
DOI: 10.1038/NATURE25014
Abstract: Cultivation-independent surveys have shown that the desert soils of Antarctica harbour surprisingly rich microbial communities. Given that phototroph abundance varies across these Antarctic soils, an enduring question is what supports life in those communities with low photosynthetic capacity. Here we provide evidence that atmospheric trace gases are the primary energy sources of two Antarctic surface soil communities. We reconstructed 23 draft genomes from metagenomic reads, including genomes from the candidate bacterial phyla WPS-2 and AD3. The dominant community members encoded and expressed high-affinity hydrogenases, carbon monoxide dehydrogenases, and a RuBisCO lineage known to support chemosynthetic carbon fixation. Soil microcosms aerobically scavenged atmospheric H
Publisher: Springer Science and Business Media LLC
Date: 27-10-2013
DOI: 10.1007/S10482-012-9835-7
Abstract: Due to the increasing atmospheric concentration of the greenhouse gas methane, more knowledge is needed on the management of methanotrophic communities. While most studies have focused on the characteristics of the methane-oxidizing bacteria (MOB), less is known about their interactions with the associated heterotrophs. Interpretative tools based on denaturing gradient gel electrophoresis allowed to evaluate the influence of copper-an important enzymatic regulator for MOB-on the activity and composition of the bacterial community. Over 30 days, enrichments with 0.1, 1.0 and 10 μM Cu(2+) respectively, showed comparable methane oxidation activities. The different copper concentrations did not create major shifts in the methanotrophic communities, as a Methylomonas sp. was able to establish dominance at all different copper concentrations by switching between both known methane monooxygenases. The associated heterotrophic communities showed continuous shifts, but over time all cultures evolved to a comparable composition, independent of the copper concentration. This indicates that the MOB selected for certain heterotrophs, possibly fulfilling vital processes such as removal of toxic compounds. The presence of a large heterotrophic food web indirectly depending on methane as sole carbon and energy source was confirmed by a clone library wherein MOB only formed a minority of the identified species.
Publisher: Springer Science and Business Media LLC
Date: 19-12-2016
DOI: 10.1038/SREP39114
Abstract: Three bioelectrochemical systems were operated with set anode potentials of +300 mV, +550 mV and +800 mV vs. Standard Hydrogen Electrode (SHE) to test the hypothesis that anode potential influences microbial ersity and is positively associated with microbial biomass and activity. Bacterial and archaeal ersity was characterized using 16 S rRNA gene licon sequencing, and biofilm thickness was measured as a proxy for biomass. Current production and substrate utilization patterns were used as measures of microbial activity and the mid-point potentials of putative terminal oxidases were assessed using cyclic voltammetry. All measurements were performed after 4, 16, 23, 30 and 38 days. Microbial biomass and activity differed significantly between anode potentials and were lower at the highest potential. Anodic electrode and electrolyte associated community composition was also significantly influenced by anode potential. While biofilms at +800 mV were thinner, transferred less charge and oxidized less substrate than those at lower potentials, they were also associated with putative terminal oxidases with higher mid-point potentials and generated more biomass per unit charge. This indicates that microbes at +800 mV were unable to capitalize on the potential for additional energy gain due to a lack of adaptive traits to high potential solid electron acceptors and/or sensitivity to oxidative stress.
Publisher: Springer Science and Business Media LLC
Date: 23-06-2021
Publisher: American Society for Microbiology
Date: 27-10-2020
DOI: 10.1128/MSYSTEMS.00658-20
Abstract: Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation.
Publisher: Springer Science and Business Media LLC
Date: 08-05-2020
DOI: 10.1038/S41598-020-64761-3
Abstract: Microorganisms employ quorum sensing (QS) mechanisms to communicate with each other within microbial ecosystems. Emerging evidence suggests that intraspecies and interspecies QS plays an important role in antimicrobial resistance in microbial communities. However, the relationship between interkingdom QS and antimicrobial resistance is largely unknown. Here, we demonstrate that interkingdom QS interactions between a bacterium, Pseudomonas aeruginosa and a yeast, Candida albicans , induce the resistance of the latter to a widely used antifungal fluconazole. Phenotypic, transcriptomic, and proteomic analyses reveal that P. aeruginosa’s main QS molecule, N-(3-Oxododecanoyl)-L-homoserine lactone, induces candidal resistance to fluconazole by reversing the antifungal’s effect on the ergosterol biosynthesis pathway. Accessory resistance mechanisms including upregulation of C. albicans drug-efflux, regulation of oxidative stress response, and maintenance of cell membrane integrity, further confirm this phenomenon. These findings demonstrate that P. aeruginosa QS molecules may confer protection to neighboring yeasts against azoles, in turn strengthening their co-existence in hostile polymicrobial infection sites.
Publisher: Frontiers Media SA
Date: 07-01-2016
Publisher: Springer Science and Business Media LLC
Date: 16-02-2015
DOI: 10.1038/SREP08496
Abstract: Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester and selective operating conditions (37°C and 55°C 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 ± 2% and 15 ± 6% of COD hydrolyzed , respectively) and dominance of Fibrobacter and Bacteroidales . Acetate accumulation ( % of COD hydrolyzed ) was also observed in the thermophilic reactors, which were dominated by Clostridium . Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis and a reduction in methane production by % of COD hydrolyzed . Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids.
Publisher: Elsevier BV
Date: 06-2014
DOI: 10.1016/J.COPBIO.2013.11.004
Abstract: Over the last decade there has been a rapid development in culture-independent techniques for exploring microbial communities, which have led to new insights into their structure and function in both natural environments and engineered systems. This review focuses on some of the most important recent advances and their applications to the erse microbial communities associated with anaerobic digestion. The use of these approaches in combination with complementary imaging techniques, chemical isotope analyses and detailed reactor performance measurements provides a new opportunity to develop a fundamental understanding of how microbial community dynamics, interactions and functionality influence digester efficiency and stability.
Publisher: Springer Science and Business Media LLC
Date: 17-04-2014
Publisher: Frontiers Media SA
Date: 24-04-2017
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.
Publisher: Wiley
Date: 18-10-2021
DOI: 10.1002/ECY.3536
Abstract: Herbivory and nutrient availability are fundamental drivers of benthic community succession in shallow marine systems, including coral reefs. Despite the importance of early community succession for coral recruitment and recovery, studies characterizing the impact of top‐down and bottom‐up drivers on micro‐ and macrobenthic communities at scales relevant to coral recruitment are lacking. Here, a combination of tank and field experiments were used to assess the effects of herbivore exclusion and nutrient enrichment on micro‐ to macrobenthic community succession and subsequent coral recruitment success. Herbivore exclusion had the strongest effect on micro‐ and macrobenthic community succession, including a community shift toward copiotrophic and potentially opportunistic athogenic microorganisms, an increased cover of turf and macroalgae, and decreased cover of crustose coralline algae. Yet, when corals settled prior to the development of a macrobenthic community, rates of post‐settlement survival increased when herbivores were excluded, benefiting from the predation refugia provided by cages during their vulnerable early post‐settlement stage. Interestingly, survival on open tiles was negatively correlated with the relative abundance of the bacterial order Rhodobacterales , an opportunistic microbial group previously associated with stressed and diseased corals. Development of micro‐ and macrobenthic communities in the absence of herbivory, however, led to reduced coral settlement. In turn, there were no differences in post‐settlement survival between open and caged treatments for corals settled on tiles with established benthic communities. As a result, open tiles experienced marginally higher recruitment rates, driven primarily by the higher initial number of settlers on open tiles compared to caged tiles. Overall, we reveal that the primary interaction driving coral recruitment is the positive effect of herbivory in creating crustose coralline algae (CCA)‐dominated habitats, free of fleshy algae and associated opportunistic microbes, to enhance coral settlement. The negative direct and indirect impact of fish predation on newly settled corals was outweighed by the positive effect of herbivory on the initial rate of coral settlement. In turn, the addition of nutrients further altered benthic community succession in the absence of herbivory, reducing coral post‐settlement survival. However, the overall impact of nutrients on coral recruitment dynamics was minor relative to herbivory.
Location: Australia
Location: Belgium
Start Date: 05-2023
End Date: 05-2026
Amount: $406,170.00
Funder: Australian Research Council
View Funded Activity