ORCID Profile
0000-0002-7437-7084
Current Organisation
University of Sydney
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Publisher: Springer Science and Business Media LLC
Date: 26-11-2021
DOI: 10.1186/S40168-021-01173-Z
Abstract: In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby “feeding” ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration ( 10 8 cells ml −1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in erse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species.
Publisher: Springer Science and Business Media LLC
Date: 09-08-2020
DOI: 10.1186/S40168-020-00889-8
Abstract: Cold environments dominate the Earth’s biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000–7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles. The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts. Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems.
Publisher: Wiley
Date: 05-2022
Abstract: Uncultivated microbial clades (‘microbial dark matter’) are inferred to play important but uncharacterized roles in nutrient cycling. Using Antarctic lake (Ace Lake, Vestfold Hills) metagenomes, 12 metagenome‐assembled genomes (MAGs 88%–100% complete) were generated for four ‘dark matter’ phyla: six MAGs from Candidatus Auribacterota (=Aureabacteria, SURF‐CP‐2), inferred to be hydrogen‐ and sulfide‐producing fermentative heterotrophs, with in idual MAGs encoding bacterial microcompartments (BMCs), gas vesicles, and type IV pili one MAG (100% complete) from Candidatus Hinthialibacterota (=OLB16), inferred to be a facultative anaerobe capable of dissimilatory nitrate reduction to ammonia, specialized for mineralization of complex organic matter (e.g. sulfated polysaccharides), and encoding BMCs, flagella, and Tad pili three MAGs from Candidatus Electryoneota (=AABM5‐125‐24), previously reported to include facultative anaerobes capable of dissimilatory sulfate reduction, and here inferred to perform sulfite oxidation, reverse tricarboxylic acid cycle for autotrophy, and possess numerous proteolytic enzymes two MAGs from Candidatus Lernaellota (=FEN‐1099), inferred to be capable of formate oxidation, amino acid fermentation, and possess numerous enzymes for protein and polysaccharide degradation. The presence of 16S rRNA gene sequences in public metagenome datasets (88%–100% identity) suggests these ‘dark matter’ phyla contribute to sulfur cycling, degradation of complex organic matter, ammonification and/or chemolithoautotrophic CO 2 fixation in erse global environments.
Publisher: American Psychological Association (APA)
Date: 2014
DOI: 10.1037/XAN0000011
Abstract: Previous research has shown rapid learning of multiple temporal relations between signals and food by pigeons when these relations are changed unpredictably each session (Kyonka & Grace, 2007). The goal of the present study was to test whether contextual temporal cues-that is, an alternative signal-food delay that was a valid predictor of a target signal-food delay-facilitated acquisition by the target contingency. Four pigeons responded in a multiple peak-interval procedure in which red and green keys signaled separate fixed-interval (FI) schedules with occasional extinction probes (peak trials). The schedule parameters of the FIs either summed to 30 s (correlated condition ρ = -1.0) or were not restricted to sum to 30 s (uncorrelated condition ρ = 0.0). Comparing stop times obtained from peak trials in the 2 conditions revealed no effect of context: Temporal control of responding was acquired at the same rate and with the same precision regardless of whether the schedule values were correlated. These results suggest that pigeons learn about multiple signal-food delays independently.
Publisher: Springer Science and Business Media LLC
Date: 30-09-2017
Publisher: Springer Science and Business Media LLC
Date: 20-06-2018
Publisher: Springer Science and Business Media LLC
Date: 13-02-2018
DOI: 10.1007/S10071-018-1168-0
Abstract: Forgetting is often thought of as the inability to remember, but remembering and forgetting allow behavior to adapt to a changing environment in distinct and separable ways. Learning and forgetting were assessed concurrently in two pigeon experiments that involved the same unconventional routine where the schedule of reinforcement changed every session. Sessions were run back-to-back with a 23-h mid-session break such that in a single visit to the testing chamber, a pigeon completed the second half of one session and the first half of the next. The beginning of a new session was either signaled or unsignaled. Experiment 1 involved concurrent variable-interval variable-interval schedules with four possible reinforcer ratios. Response allocation was sensitive to the richer schedule and was retained through the mid-session break. Experiment 2 involved peak interval schedules of varying durations. Temporal discrimination was rapidly acquired before and after the mid-session break, but not retained. Signaling the session change decreased control by past contingencies in both experiments, demonstrating that learning and forgetting can be investigated separately. These results suggest that the temporal structure of training, such as multiple short daily sessions instead of one long session, can meaningfully impact measurement of animals' capacity to forget and remember.
Publisher: Springer Science and Business Media LLC
Date: 02-12-2022
DOI: 10.1186/S40168-022-01404-X
Abstract: Ace Lake is a marine-derived, stratified lake in the Vestfold Hills of East Antarctica with an upper oxic and lower anoxic zone. Cyanobacteria are known to reside throughout the water column. A Synechococcus -like species becomes the most abundant member in the upper sunlit waters during summer while persisting annually even in the absence of sunlight and at depth in the anoxic zone. Here, we analysed ~ 300 Gb of Ace Lake metagenome data including 59 Synechococcus -like metagenome-assembled genomes (MAGs) to determine depth-related variation in cyanobacterial population structure. Metagenome data were also analysed to investigate viruses associated with this cyanobacterium and the host’s capacity to defend against or evade viruses. A single Synechococcus -like species was found to exist in Ace Lake, Candidatus Regnicoccus frigidus sp. nov., consisting of one phylotype more abundant in the oxic zone and a second phylotype prevalent in the oxic-anoxic interface and surrounding depths. An important aspect of genomic variation pertained to nitrogen utilisation, with the capacity to perform cyanide assimilation and asparagine synthesis reflecting the depth distribution of available sources of nitrogen. Both specialist (host specific) and generalist (broad host range) viruses were identified with a predicted ability to infect Ca. Regnicoccus frigidus. Host-virus interactions were characterised by a depth-dependent distribution of virus type (e.g. highest abundance of specialist viruses in the oxic zone) and host phylotype capacity to defend against (e.g. restriction-modification, retron and BREX systems) and evade viruses (cell surface proteins and cell wall biosynthesis and modification enzymes). In Ace Lake, specific environmental factors such as the seasonal availability of sunlight affects microbial abundances and the associated processes that the microbial community performs. Here, we find that the population structure for Ca. Regnicoccus frigidus has evolved differently to the other dominant phototroph in the lake, Candidatus Chlorobium antarcticum. The geography (i.e. Antarctica), limnology (e.g. stratification) and abiotic (e.g. sunlight) and biotic (e.g. microbial interactions) factors determine the types of niches that develop in the lake. While the lake community has become increasingly well studied, metagenome-based studies are revealing that niche adaptation can take many paths these paths need to be determined in order to make reasonable predictions about the consequences of future ecosystem perturbations.
No related grants have been discovered for Pratibha Panwar.