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Time-series measurements of size fractionated primary production (>3 micron) in the subtropical North Pacific Ocean

Filter size-fractionated (>3 μm) particulate 14C-based rates of primary production were measured at six discrete depths (5, 25, 45, 75, 100, and 125 m) throughout the euphotic zone. Seawater samples from each depth were subsampled into triplicate 30-mL polycarbonate centrifuge tubes from a pre-dawn cast, inoculated with 70 µL of NaH14CO3-, then incubated over the full photoperiod (~12-14 hours) on a floating in situ array at the corresponding depths where the water was collected. At the end of the incubation period (after sundown), 25 mL of each sample was vacuum-filtered first onto a 25-mm diameter 3-μm pore size polycarbonate membrane.

Time-series measurements of size fractionated primary production (14C-assimilation) in the subtropical North Pacific Ocean

Filter size-fractionated (>0.2-3 μm) particulate 14C-based rates of primary production were measured at six discrete depths (5, 25, 45, 75, 100, and 125 m) throughout the euphotic zone. Seawater samples from each depth were subsampled into triplicate 30-mL polycarbonate centrifuge tubes from a pre-dawn cast, inoculated with 70 µL of NaH14CO3-, then incubated over the full photoperiod (~12-14 hours) on a floating in situ array at the corresponding depths where the water was collected. At the end of the incubation period (after sundown), 25 mL of each sample was vacuum-filtered first onto a 25-mm diameter 3-μm pore size polycarbonate membrane, then the filtrate was vacuum-filtered onto a 25-mm diameter 0.2-μm pore size polycarbonate membrane filter. The rates reported here are for the >0.2-3 μm size fraction.

Time series measurements of leucine incorporation as a measure of bacterial production in the subtropical North Pacific Ocean

Samples were collected at or in the vicinity of Station ALOHA on 24 different cruises. On each cruise, rates of 3H-Leu incorporation into protein were measured. Seawater samples for measurements of production were collected from pre-dawn vertical hydrocasts at 6 discrete depths (5, 25, 45, 75, 100, 125 m) using polyvinyl chloride sampling bottles affixed to a rosette sampler. Polyethylene amber bottles (125 ml capacity) were subsampled from the CTD rosette bottles, and duplicate acid-cleaned 12 ml polycarbonate centrifuge tubes were filled from each depth. Each polycarbonate tube was inoculated with 20 nmol L-1 (final concentration) 3,4,5-3H-leucine. An additional 1.5 ml per depth was subsampled into 2 ml microcentrifuge tubes  containing 100 µl of 100% (w/v) ice-cold trichloroacetic acid (TCA) to serve as a killed blank. The polycarbonate sample tubes were capped and incubated in situ over the photoperiod to measure rates of 3H-Leu incorporation in both dark (through use of black cloth bags) and light on a free-drifting array. At the end of the photoperiod, triplicate 1.5 ml subsamples were removed from each tube and added to 2 ml microcentrifuge tubes containing 100 µl of 100% ice-cold TCA; these tubes were stored frozen until analysis. Samples were processed following a modified method of the microcentrifuge method.

Time-series rates of dissolved organic carbon production in the subtropical North Pacific Ocean

Over a 3-year period (April 2010-April 2013), we measured 14C-DOC production from vertical profiles used for determination of 14C-particle production, utilizing 0.2 um filtrates. Seawater for these experiments was collected from predawn CTD hydrocasts into acid-cleaned 500-ml polycarbonate bottles. A total of four replicate 500 ml bottles were subsampled per depth and each bottle was spiked with ~1.85 MBq 14C-bicarbonate. One hundred milliliters from one replicate per depth was vacuum filtered through a 0.2 mm polycarbonate filter and the filtrate served as a time zero blank. The remaining three bottles were hung on a free-drifting array, deployed before dawn, and incubated at their initial collection depths throughout the photoperiod (typically 11-13 hours). After sunset the array was recovered, and 100 ml subsamples of all bottles were filtered under gentle vacuum (<50 mm Hg) onto 0.2 mm polycarbonate filters. These 0.2 mm filtrates were stored frozen (-20oC) until subsequent processing for determination of 14C-DOC productivity. Samples were processed as follows: 100 ml of the 14C-PC filtrates were thawed, poured into 500 ml polyethylene separatory funnels, and acidified by the addition of 500 µl of 2 M sulfuric acid (H2SO4). Samples were vigorously bubbled with air in a fume hood to remove 14CO2. A 70 ml subsample was removed from each separatory funnel and poured into a 100 ml glass serum bottle containing 1 ml of 2 M sodium hydroxide (NaOH) and 10 ml of 0.37 M potassium persulfate (K2S2O8) in 1 M NaOH. Bottles were sealed with rubber stoppers, crimp sealed with an aluminum cap, and autoclaved at 126°C for 200 minutes; oxidizing 14C-DOC to 14C-DIC in an alkaline solution. Once cooled to room temperature, samples were uncapped and resealed using rubber sleeve stoppers holding plastic center wells containing ~2 x 2 cm pieces of fluted chromatographic filter paper (Whatman 2) soaked with 0.2 ml of β-phenylethylamine. A syringe was used to inject 4 ml of 9 N H2SO4 into the solution, converting the 14C-labeled dissolved inorganic carbon (hereafter 14C-DIC) to 14CO2. Samples were stored undisturbed at room temperature, passively trapping the 14CO2 on the β-phenylethylamine soaked wick. After at least 100 hours, rubber sleeve stoppers were removed and center wells and wicks were placed in scintillation vials, followed by the addition of 10 ml of Ultima Gold LLT scintillation cocktail. Samples were subsequently counted on a Perkin Elmer Tri-Carb 2800TR liquid scintillation counter. Rates of 14C-DOC production were computed for each cruise as the mean of the triplicate bottles from each depth minus the average 14C-activity of the time zero (blank) samples.

Time series measurements of 14C-based primary production (>0.2 um) in the subtropical North Pacific Ocean

Over a 3-year period (April 2010-April 2013), we measured primary production from vertical profiles at near-monthly time scales in the subtropical North Pacific Ocean. Production measurements were based on 14C-assimilation into  >0.2 um plankton biomass.  Seawater for the productivity measurements was collected from predawn CTD hydrocasts into acid-cleaned 500-ml polycarbonate bottles. A total of four replicate 500 ml bottles were subsampled per depth and each bottle was spiked with ~1.85 MBq 14C-bicarbonate. One hundred milliliters from one replicate per depth was immediately vacuum filtered through a polycarbonate filter as a time zero blank. These filters were placed in 20 ml glass scintillation vials and stored at -20oC until shore-based laboratory processing. The remaining three bottles were hung on a free-drifting array, deployed before dawn, and incubated at their initial collection depths throughout the photoperiod (typically 11-13 hours). After sunset the array was recovered, and 100 ml subsamples of all bottles were filtered under gentle vacuum onto 0.2 um polycarbonate filters that were then placed in scintillation vials and frozen. The total radioactivity added to each sample bottle was determined by subsampling 250 µl aliquots into scintillation vials containing 500 µl of β-phenylethylamine. At the shore-based laboratory, filters were acidified, passively vented, and the resulting radioactivity was determined using liquid scintillation counting.

Time series measurements of nitrogen fixation in the subtropical North Pacific

Rates of N2 fixation were measured using the 15N2 isotopic tracer technique. Sampling occurred during near-monthly Hawaii Ocean Time-series cruises. Whole seawater samples from six discrete depths (5, 25, 45, 75, 100, and 125 m) were subsampled into acid-washed 4.3 L polycarbonate bottles.  Between June 2005 and May 2012, 3 mL of 15N2 gas was injected into each bottle.  Beginning in August 2012, the 15N2 gas was first dissolved into seawater and 100 mL of the resulting 15N2-enriched water was added to 4.3 L polycarbonate sampling bottles. The resulting atom % enrichment of stocks of 15N2-enriched seawater was measured using a membrane inlet mass spectrometer. Incubation bottles amended with the 15N2 tracer were attached to a free-drifting array and incubated at the discrete depths from which samples had been collected. The array was deployed before dawn and samples were incubated at in situ light and temperature for 24 h. After recovery of the array, the entire volume from each bottle was filtered onto a pre-combusted glass microfiber filter (Whatman 25 mm GF/F) and filters were placed onto pre-combusted pieces of foil in Petri dishes and stored frozen at -20°C. Filters were dried for 24 h at 60°C, pelleted, and the total mass of N and its isotopic signature on each filter were analyzed on an elemental analyzer-isotope ratio mass spectrometer (Carlo-Erba EA NC2500 coupled with ThermoFinnigan Delta S).

opencc-by-4.0Apr 2020View details →

Deep sea dissolved organic nitrogen and phosphorus (DON and DOP) at Station ALOHA in the North Pacific Subtropical Gyre

Data on organic and inorganic nutrients in unfiltered seawater that was sampled at and around Station ALOHA, north of Oahu, Hawaii, in the North Pacific Subtropical Gyre. Seawater was collected into HDPE or polypropylene bottles and immediately frozen. Silicate, phosphate and nitrate+nitrite are determined colormetrically on a SEAL Analytical Autoanalyzer (AA3 with HR detectors), with the exception of nitrate+nitrite that is <0.5umol/L, which is analyzed by high-sensitivity chemiluminescence. Total phosphorus (TP) and total nitrogen (TN) are determined by analysis of phosphate and nitrate, respectively, after oxidation by high-intensity ultraviolet light. Total organic phosphorus and total organic nitrogen are determined by subtracting background PO4 and NO3+NO2 from TP and TN, respectively. Total organic carbon is determined by combustion on a Shimadzu TOC-V analyzer. This dataset was originally published in the following article, in which additional details and interpretations of the data can be found: R. K. Foreman, K. M. Björkman, C. A. Carlson, K. Opalk, D. M. Karl, (2019). Improved ultraviolet photo‐oxidation system yields estimates for deep‐sea dissolved organic nitrogen and phosphorus,  Limnol. Oceanogr. Methods, <a href="https://doi.org/10.1002/lom3.10312">doi.org/10.1002/lom3.10312</a>

opencc-by-4.0Apr 2020View details →

Subtropical Front diagnostics in eORCA025 and NZ20

This tar ball contains all relevant data which is used to prepare the draft manuscript Seasonal and interannual variability of the Subtropical Front in the New Zealand region. Individual folders are used for the individual diagnostics and models. The STF numpy arrays contain the location for the STF using the detection algorithm. The order in the in the array is STF_salt : lat_low, depth_low, lat, depth, lat_high,depth_high, STF_salt : lat_low, depth_low, lat, depth, lat_high,depth_high and lon. The detection is based on monthly means starting in 1980, or 2004 for Argo.

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Genomic evidence of introgression and adaptation in a model subtropical tree species, Eucalyptus grandis

The genetic consequences of adaptation to changing environments can be deciphered using landscape genomics, which may help predict species' responses to global climate change. Towards this, we used genome-wide SNP marker analysis to determine population structure and patterns of genetic differentiation in terms of neutral and adaptive genetic variation in the natural range of Eucalyptus grandis, a widely cultivated subtropical and temperate species, serving as genomic reference for the genus. We analysed introgression patterns at subchromosomal resolution using a modified ancestry mapping approach and identified provenances with extensive interspecific introgression, suggesting early hybrid speciation in response to increased aridity. Furthermore, we describe potentially adaptive genetic variation as explained by environment-associated SNP markers, which also led to the discovery of a large structural variant. Finally, we show that genes linked to these markers are enriched for biotic and abiotic stress responses.

opencc-zeroNov 2020View details →

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The U-shaped pattern of size-dependent mortality and its driving factors in a subtropical monsoon evergreen forest

1. Tree mortality is an important ecological process influencing multiple functions of forest ecosystems. Previous studies have shown two basic size-mortality patterns, including a competition-driven declining and a disturbance-driven increasing mortality rate with tree size. Subtropical forests, which have a high species diversity and subject to frequent monsoon disturbances, are widely distributed in eastern Asia. However, the tree size-mortality pattern in the mature subtropical forests remains unclear. 2. Here we analyzed patterns of size-dependent mortality from tree species to forest community using a 5-year inventory data from 117 species and 163,612 individuals in a 20-ha forest dynamic plot in a mature subtropical monsoon evergreen forest in eastern China. To explain the spatial variability in mortality patterns, two major biotic drivers (competition and tree size) and multiple local-scale environmental factors were further analyzed. 3. Our results showed that tree size was the best predictor of tree mortality at the scales of both species and community. A species-level analysis identified four size-mortality patterns that are shaped by species-specific attributes such as maximum size and life form. For 27 out of 92 species that comprised 59% of tree individuals, the relationship between size and mortality exhibited a U-shaped pattern of a first decline followed by an increase. An overall community-scale size-dependent mortality also showed a U-shaped pattern. 4. Tree mortality was also influenced by the competition and environmental conditions, but the relative importance varied widely across tree sizes and species. The competition showed significant correlations with the mortality of small trees, while the effect of environmental conditions on mortality was strongest for large trees. A principal component analysis showed that a combination of biotic and abiotic factors explained 42.3% of the spatial variation in mortality at large sizes. Synthesis. Our results reveal four identifiable size-dependent mortality patterns that differ across diverse species, jointly leading to a U-shaped mortality size pattern at the community level. This finding calls for the need to establish the details of every potential size-mortality pattern with consideration of the different effects of biotic and abiotic factors on tree mortality of specific size.

opencc-zeroNov 2020View details →

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Data from: Regime shifts in an Early Triassic subtropical ecosystem

The Early Triassic was one of the most remarkable time intervals in Earth History. To begin with, life on Earth had to face one of the largest subaerial volcanic degassing, the Siberian Traps, followed by a plethora of accompanying environmental hazards with pronounced and repeated climatic changes. These changes not only led to repeated and, for several marine nektonic clades, intense extinction events but also to significant changes in terrestrial ecosystems. The Early Triassic terrestrial ecosystems of the southern subtropical region (Pakistan) are not necessarily marked by abrupt extinction events but by extreme shifts in composition. Modern ecological theories describe such shifts as catastrophic regime shifts. Here, the applicability of modern ecological theories to these past events is tested. Abrupt shifts in ecosystems can occur when protracted changing abiotic drivers (e.g. climate) reach critical points (thresholds or tipping points) sometimes accentuated by stochastic events. Early Triassic terrestrial plant ecosystem changes stand out from the longer term paleobotanical records because changes of similar magnitude have not been observed for many millions of years before and after the Early Triassic. To date, these changes have been attributed to repeated severe environmental perturbations, but here an alternative explanation is tested: the initial environmental perturbations around the Permian–Triassic boundary interval are regarded here as a main cause for a massive loss in terrestrial ecosystem resilience with the effect that comparatively small-scale perturbations in the following ~5 Ma lead to abrupt regime shifts in terrestrial ecosystems.

opencc-zeroNov 2020View details →

opennotspecifiedNov 2020View details →

FIGURE 1 in Morphology of testate amoeba Difflugia australis (Playfair, 1918) Gautier-Lièvre et Thomas, 1958 from a subtropical reservoir (southeast China)

FIGURE 1. Morphometric characteristics of Difflugia australis from Shidou Reservoir, Xiamen, China. (A) Shell outline (lateral and apertural views) showing covering of irregularly shaped, flat particles and position of measured morphometric axes in this study. 1–total shell length, 2–shell width, 3–aperture diameter, 4–collar height, 5–body length, 6–spine length. (B) Frequency plots of shell dimensions. Histograms showing the size frequency of aperture diameter (left column), shell width (middle column) and total shell length (right column). (C) Frequency plots of mineral dimensions. Histograms showing the size frequency of apertural mineral perimeter (left column), body mineral perimeter (middle column) and spine mineral perimeter (right column).

opennotspecifiedNov 2020View details →

FIGURE 4 in Morphology of testate amoeba Difflugia australis (Playfair, 1918) Gautier-Lièvre et Thomas, 1958 from a subtropical reservoir (southeast China)

FIGURE 4. The shell elemental composition of Difflugia australis as measured in full scale X-Ray on aperture (A), body (B) and spine (C) sections. The scale bars are 10 μm.

FIGURES 78-80 in The open-holed trapdoor spiders (Mygalomorphae: Anamidae: Namea) of Australia's D'Aguilar Range: revealing an unexpected subtropical hotspot of rainforest diversity

FIGURES 78-80. Namea nebo sp. nov., male holotype (QMB S65274) from Mount Nebo (south-eastern Queensland), pedipalp: 78, retrolateral view; 79, retroventral view; 80, prolateral view. Scale bar = 3.0 mm.

FIGURES 55–64 in The open-holed trapdoor spiders (Mygalomorphae: Anamidae: Namea) of Australia's D'Aguilar Range: revealing an unexpected subtropical hotspot of rainforest diversity

FIGURES 55–64. Namea nigritarsus sp. nov., male holotype (QMB S111534) from Mount Glorious (south-eastern Queensland), somatic morphology: 55–56, carapace and abdomen, dorsal view; 57, cephalothorax, lateral view; 58, eyes, dorsal view; 59, mouthparts, ventral view; 60–61, cephalothorax and abdomen, ventral view; 62, leg I, prolateral view; 63, leg I tibia, retrolateral view; 64, leg I tibia, profile in standardised prolateral view, showing relative position of macrosetae (p, prolateral; pd, prodorsal; pv, proventral; v, ventral). Scale bars = 3.0 mm.

FIGURES 45–47 in The open-holed trapdoor spiders (Mygalomorphae: Anamidae: Namea) of Australia's D'Aguilar Range: revealing an unexpected subtropical hotspot of rainforest diversity

FIGURES 45–47. Namea gowardae sp. nov., male holotype (QMB S774) from Mount Glorious (south-eastern Queensland), pedipalp: 45, retrolateral view; 46, retroventral view; 47, prolateral view. Scale bar = 3.0 mm.

FIGURES 35–44 in The open-holed trapdoor spiders (Mygalomorphae: Anamidae: Namea) of Australia's D'Aguilar Range: revealing an unexpected subtropical hotspot of rainforest diversity

FIGURES 35–44. Namea gowardae sp. nov., male holotype (QMB S774) from Mount Glorious (south-eastern Queensland), somatic morphology: 35–36, carapace and abdomen, dorsal view; 37, cephalothorax, lateral view; 38, eyes, dorsal view; 39, mouthparts, ventral view; 40–41, cephalothorax and abdomen, ventral view; 42, leg I, prolateral view (inset shows detail of tibia, and the location of the 'tibial bald zone'); 43, leg I tibia, retrolateral view; 44, leg I tibia, profile in standardised prolateral view, showing relative position of macrosetae (pd, prodorsal; pv, proventral; v, ventral); note the broken seta (*) at position pv1. Scale bars = 3.0 mm.

FIGURES 32–34 in The open-holed trapdoor spiders (Mygalomorphae: Anamidae: Namea) of Australia's D'Aguilar Range: revealing an unexpected subtropical hotspot of rainforest diversity

FIGURES 32–34. Namea gloriosa sp. nov., male holotype (QMB S10269) from Mount Glorious (south-eastern Queensland), pedipalp: 32, retrolateral view; 33, retroventral view; 34, prolateral view. Scale bar = 3.0 mm.

FIGURES 65–67 in The open-holed trapdoor spiders (Mygalomorphae: Anamidae: Namea) of Australia's D'Aguilar Range: revealing an unexpected subtropical hotspot of rainforest diversity

FIGURES 65–67. Namea nigritarsus sp. nov., male holotype (QMB S111534) from Mount Glorious (south-eastern Queensland), pedipalp: 65, retrolateral view; 66, retroventral view; 67, prolateral view. Scale bar = 3.0 mm.

FIGURES 14–21 in The open-holed trapdoor spiders (Mygalomorphae: Anamidae: Namea) of Australia's D'Aguilar Range: revealing an unexpected subtropical hotspot of rainforest diversity

FIGURES 14–21. Comparative morphology of Namea from the D'Aguilar Range (south-eastern Queensland); each figure for each species depicts (a) the male tibia I in standardised prolateral view, (b) the male pedipalp in retrolateral view, +/- (c) the female cleared genitalia in dorsal view (if known): 14, N. gloriosa sp. nov. (QMB S10269); 15, N. nigritarsus sp. nov. (QMB S111534); 16, N. nebo sp. nov. (QMB S65274); 17, N. excavans Raven, 1984 (QMB S813); 18, N. brisbanensis Raven, 1984 (QMB S767 [male], S111397 [female]); 19, N. gowardae sp. nov. (QMB S774 [male], S111377 [female]); 20, N. salanitri Raven, 1984 (QMB S1166 [male], S111396 [female; with epigastric lobes highlighted*); 21, N. dahmsi Raven, 1984 (QMB S88018 [male tibia I], S800 [male pedipalp], S111481 [female; note bent right spermathecal fundus]). Tibial macrosetae are coloured and labelled according to their relative position (dark blue, prodorsal [pd]; red, prolateral [p] or proventral [pv]; dark grey, ventral [v]; light blue, retroventral [rv]).