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- ItemCopper induces nitrification by ammonia-oxidizing bacteria and archaea in pastoral soils(Wiley, 2022-12-12) Matse D; Jeyakumar P; Bishop P; Anderson CCopper (Cu) is the main co-factor in the functioning of the ammonia monooxygenase (AMO) enzyme, which is responsible for the first step of ammonia oxidation. We report a greenhouse-based pot experiment that examines the response of ammonia-oxidizing bacteria and archaea (AOB and AOA) to different bioavailable Cu concentrations in three pastoral soils (Recent, Pallic, and Pumice soils) planted with ryegrass (Lolium perenne L.). Five treatments were used: control (no urine and Cu), urine only at 300 mg N kg-1 soil (Cu0), urine + 1 mg Cu kg-1 soil (Cu1), urine + 10 mg Cu kg-1 soil (Cu10), and urine + 100 mg Cu kg-1 soil (Cu100). Pots were destructively sampled at Day 0, 1, 7, 15, and 25 after urine application. The AOB/AOA amoA gene abundance was analyzed by real-time quantitative polymerase chain reaction at Days 1 and 15. The AOB amoA gene abundance increased 10.0- and 22.6-fold in the Recent soil and 2.1- and 2.5-fold in the Pallic soil for the Cu10 compared with Cu0 on Days 1 and 15, respectively. In contrast, the Cu100 was associated with a reduction in AOB amoA gene abundance in the Recent and Pallic soils but not in the Pumice soil. This may be due to the influence of soil cation exchange capacity differences on the bioavailable Cu. Bioavailable Cu in the Recent and Pallic soils influenced nitrification and AOB amoA gene abundance, as evidenced by the strong positive correlation between bioavailable Cu, nitrification, and AOB amoA. However, bioavailable Cu did not influence the nitrification and AOA amoA gene abundance increase.
- ItemEvaluating edge-of-range genetic patterns for tropical echinoderms, Acanthaster planci and Tripneustes gratilla, of the Kermadec Islands, southwest Pacific(ROSENSTIEL SCH MAR ATMOS SCI, 2014-01-01) Liggins L; Gleeson L; Riginos CEdge-of-range populations are often typified by patterns of low genetic diversity and high genetic differentiation relative to populations within the core of a species range. The "core-periphery hypothesis," also known as the "central-marginal hypothesis," predicts that these genetic patterns at the edge-of-range are a consequence of reduced population size and connectivity toward a species range periphery. It is unclear, however, how these expectations relate to high dispersal marine species that can conceivably maintain high abundance and high connectivity at their range edge. In the present study, we characterize the genetic patterns of two tropical echinoderm populations in the Kermadec Islands, the edge of their southwest Pacific range, and compare these genetic patterns to those from populations throughout their east Indian and Pacific ranges. We find that the populations of both Acanthaster planci (Linnaeus, 1758) and Tripneustes gratilla (Linnaeus, 1758) are represented by a single haplotype at the Kermadec Islands (based on mitochondrial cytochrome oxidase C subunit I). Such low genetic diversity concurs with the expectations of the "core-periphery hypothesis." Furthermore, the haplotypic composition of both populations suggests they have been founded by a small number of colonists with little subsequent immigration. Thus, local reproduction and self-recruitment appear to maintain these populations despite the ecologically marginal conditions of the Kermadec Islands for these tropical species. Understanding rates of self-recruitment vs reliance on connectivity with populations outside of the Kermadec Islands has implications for the persistence of these populations and range stability of these echinoderm species.© 2014 Rosenstiel School of Marine and Atmospheric Science of the University of Miami.
- ItemMorphological and genetic divergence supports peripheral endemism and a recent evolutionary history of Chrysiptera demoiselles in the subtropical South Pacific(2022-06-01) Liggins L; Kilduff L; Trnski T; Delrieu-Trottin E; Carvajal JI; Arranz V; Planes S; Saenz-Agudelo P; Aguirre JDThe delineation of species and their evolutionary relationships informs our understanding of biogeography and how regional faunas are assembled. The peripheral geography and local environment of reefs in the subtropical South Pacific likely promotes the allopatric and adaptive divergence of taxa colonising from the tropics; however, the fauna of this region has been relatively understudied. Here, we address the taxonomic and evolutionary relationships among Chrysiptera taxa of the subtropical South Pacific. We use meristic counts, morphometrics and genetic markers to characterise the similarities and differences among four taxa restricted to the South Pacific region that have strikingly different colouration: C. notialis, a taxon restricted to eastern Australia, New Caledonia, Lord Howe Island and Norfolk Island; C. galba, found in the Cook Islands, southern French Polynesia and Pitcairn Islands; and the two disjunct populations of C. rapanui, found in the eastern Pacific around Rapa Nui (Isla de Pascua or Easter Island) and Motu Motiro Hiva (Salas y Gómez) and in the South-western Pacific around Rangitāhua (Kermadec Islands). Our morphometric analysis confirmed that these four taxa, including the two disjunct populations of C. rapanui, are morphologically distinct. However, our genetic analysis revealed that only C. rapanui from Rapa Nui was genetically differentiated, whereas C. rapanui of Rangitāhua, C. galba and C. notialis all shared a common haplotype. Furthermore, none of the taxa could be consistently differentiated based on individual meristic features. Our study reconciles a formerly perplexing and disjunct distribution for C. rapanui, to reveal that C. rapanui is an endemic of Rapa Nui and that the Chrysiptera of French Polynesia, Rangitāhua, and the South-western Pacific have only a very recent history of divergence. Our analyses suggest these subtropical taxa have diverged from a predominantly tropical Chrysiptera genus in morphological features important in determining colonisation success, locomotion and feeding ecology.
- ItemResponses of rice (Oryza sativa L.) plant growth, grain yield and quality, and soil properties to the microplastic occurrence in paddy soil(Springer, 2022-05-18) Chen S; Feng Y; Han L; Li D; Feng Y; Jeyakumar P; Sun H; Shi W; Wang HPurpose: Agricultural soil has been recognized as a major sink of microplastic, an emerging pollutant to environmental biodiversity and ecosystem. However, the impacts of microplastic on soil–plant systems (e.g., crop growth, grain yield and amino acid content, nitrogen uptake capacity, and soil properties) remain largely unknown. Methods: Four typical microplastics, i.e., polythene (PE, 200 μm), polyacrylonitrile (PAN, 200 μm), and polyethylene terephthalate (PET) in diameter of 200 μm and 10 μm (PET200 and PET10), were tested to assess the consequent aforementioned responses under rice (Oryza sativa L.) paddy soil in a mesocosm experiment. Results: Microplastics multiply influenced the soil pH, NH4+-N and NO3−-N contents, which effects were depended on the rice growth stage and plastic type. Overall, microplastics significantly decreased the soil urease activity by 5.0–12.2% (P < 0.05). When exposed to PAN and PET (in both diameter of 200 μm and 10 μm), there were significantly 22.2–30.8% more grain yield produced, compared to the control (P < 0.05), which was attributing to the higher nitrogen uptake capacity of rice grain. Meanwhile, microplastics exhibited nominal influences on rice plant height, tillering number, leaf SPAD, and NDVI. The amino acids were affected by microplastic, depending on the types of plastics and amino acids. Conclusion: This study provides evidence that microplastic can affect the development and final grain yield, amino acid content, nitrogen uptake capacity of rice, and some major soil properties, while these effects vary as a function of plastic type. Our findings highlight the positive impacts that could occur when the presence of microplastics in paddy soil.
- ItemRetrofitting home insulation reduces incidence and severity of chronic respiratory disease(John Wiley and Sons, Ltd, 2022-08-21) Fyfe C; Barnard LT; Douwes J; Howden-Chapman P; Crane JTo assess whether retrofitting home insulation can reduce the risk of respiratory disease incidence and exacerbation, a retrospective cohort study was undertaken using linked data from a national intervention program. The study population was made up of 1 004 795 residents from 205 001 New Zealand houses that received an insulation subsidy though a national Energy Efficiency and Conservation Authority program. A difference-in-difference model compared changes in the number of prescriptions dispensed for respiratory illness post- insulation to a control population over the same timeframe. New prescribing of chronic respiratory disease medication at follow-up was used to compare incidence risk ratios between intervention and control groups. Chronic respiratory disease incidence was significantly lower in the intervention group at follow-up: odds ratio 0.90 (95% CI: 0.86-0.94). There was also a 4% reduction in medication dispensed for treating exacerbations of chronic respiratory disease symptoms in the intervention group compared with the control group: relative rate ratio (RRR) 0.96 (95% CI: 0.96-0.97). There was no change in medication dispensed to prevent symptoms of chronic respiratory disease RRR: 1,00 (95% CI: 0.99-1.00). These findings support home insulation interventions as a means of improving respiratory health outcomes.
- ItemReturn of the ghosts of dispersal past: Historical spread and contemporary gene flow in the blue sea star Linckia laevigata(ROSENSTIEL SCH MAR ATMOS SCI, 2014-01-01) Crandall ED; Treml EA; Liggins L; Gleeson L; Yasuda N; Barber PH; Wörheide G; Riginos CMarine animals inhabiting the Indian and Pacific oceans have some of the most extensive species ranges in the world, sometimes spanning over half the globe. These Indo-Pacific species present a challenge for study with both geographic scope and sampling density as limiting factors. Here, we augment and aggregate phylogeographic sampling of the iconic blue sea star, Linckia laevigata Linnaeus, 1758, and present one of the most geographically comprehensive genetic studies of any Indo-Pacific species to date, sequencing 392 base pairs of mitochondrial COI from 791 individuals from 38 locations spanning over 14,000 km. We first use a permutation based multiple-regression approach to simultaneously evaluate the relative influence of historical and contemporary gene flow together with putative barriers to dispersal. We then use a discrete diffusion model of phylogeography to infer the historical migration and colonization routes most likely used by L. laevigata across the Indo-Pacific. We show that estimates of genetic structure have a stronger correlation to geographic distances than to "oceanographic" distances from a biophysical model of larval dispersal, reminding us that population genetic estimates of gene flow and genetic structure are often shaped by historical processes. While the diffusion model was equivocal about the location of the mitochondrial most recent common ancestor (MRC A), we show that gene flow has generally proceeded in a step-wise manner across the Indian and Pacific oceans. We do not find support for previously described barriers at the Sunda Shelf and within Cenderwasih Bay. Rather, the strongest genetic disjunction is found to the east of Cenderwasih Bay along northern New Guinea. These results underscore the importance of comprehensive range-wide sampling in marine phylogeography.© 2014 Rosenstiel School of Marine and Atmospheric Science of the University of Miami.
- ItemSeascape features, rather than dispersal traits, predict spatial genetic patterns in co-distributed reef fishes(Wiley, 2015) Liggins L; Treml EA; Possingham HP; Riginos CAim: To determine which seascape features have shaped the spatial genetic patterns of coral reef fishes, and to identify common patterns among species related to dispersal traits [egg type and pelagic larval duration (PLD)]. Location: Indian and Pacific Oceans, including the Indo-Australian Archipelago. Methods: We sampled coral reef fishes with differing dispersal traits (Pomacentrus coelestis, Dascyllus trimaculatus, Hailchoeres hortulanus and Acanthurus triostegus) and characterized spatial (mtDNA) genetic patterns using AMOVA-clustering and measures of genetic differentiation. Similarity in the spatial genetic patterns among species was assessed using the congruence among distance matrices method and the seascape features associated with the genetic differentiation of each species were identified using multiple regression of distance matrices (MRDM) and stepwise model selection. Results: Similar spatial genetic patterns were found for P. coelestis and H. hortulanus, despite their differing egg type (benthic versus pelagic). MRDM indicated that geographical distance was underlying their correlated genetic patterns. Species with pelagic eggs (A. triostegus and H. hortulanus) also had correlated patterns of genetic differentiation (Dest); however, a common underlying seascape feature could not be inferred. Additionally, the common influence of the Torres Strait and the Lydekker/Weber's line was identified for the genetic patterns of differentiation for P. coelestis and A. triostegus, despite their differing dispersal traits, and the uncorrelated spatial genetic patterns of these species. Main conclusions: Our study demonstrates the value of a quantitative, hypothesis-testing framework in comparative phylogeography. We found that dispersal traits (egg type and PLD) did not predict which species had similar spatial genetic patterns or which seascape features were associated with these patterns. Furthermore, even in the absence of visually similar, or correlated spatial genetic patterns, our approach enabled us to identify seascape features that had a common influence on the spatial genetic patterns of co-distributed species.
- ItemSoil properties impacting denitrifier community size, structure and activity in New Zealand dairy-grazed pastures(Copernicus Publications, 2017-09-22) Jha N; Saggar S; Giltrap D; Tillman R; Deslippe J; N/AAbstract. Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N 2 O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N O emissions through denitrification are likely to be most im- 2 2 2 portant for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N O emissions through denitrification across a wide range of soil types.
- ItemVicariance and dispersal across an intermittent barrier: Population genetic structure of marine animals across the Torres Strait land bridge(SPRINGER, 2011-12-01) Mirams AGK; Treml EA; Shields JL; Liggins L; Riginos CBiogeographic barriers, some transitory in duration, are likely to have been important contributing factors to modern marine biodiversity in the Indo-Pacific region. One such barrier was the Torres Strait land bridge between continental Australia and New Guinea that persisted through much of the late Pleistocene and separated Indian and Pacific Ocean taxa. Here, we examine the patterns of mitochondrial DNA diversity for marine animals with present-day distributions spanning the Torres Strait. Specifically, we investigate whether there are concordant signatures across species, consistent with either vicariance or recent colonization from either ocean basin. We survey four species of reef fishes (Apogon doederleini, Pomacentrus coelestis, Dascyllus trimaculatus, and Acanthurus triostegus) for mtDNA cytochrome oxidase 1 and control region variation and contrast these results to previous mtDNA studies in diverse marine animals with similar distributions. We find substantial genetic partitioning (estimated from F-statistics and coalescent approaches) between Indian and Pacific Ocean populations for many species, consistent with regional persistence through the late Pleistocene in both ocean basins. The species-specific estimates of genetic divergence, however, vary greatly and for reef fishes we estimate substantially different divergence times among species. It is likely that Indian and Pacific Ocean populations have been isolated for multiple glacial cycles for some species, whereas for other species genetic connections have been more recent. Regional estimates of genetic diversity and directionality of gene flow also vary among species. Thus, there is no apparent consistency among historical patterns across the Torres Strait for these co-distributed marine animals. © 2011 Springer-Verlag.