Lynnath Beckley

This virtual special issue of Deep-Sea Research II is the seventh volume of scientific papers arising from the Second International Indian Ocean Expedition (IIOE-2, Fig. 1). This diverse body of research from the Indian Ocean encompasses papers on marine geology, physical, chemical, and biological oceanography, as well as paleoceanography. This volume represents another important step toward achieving the overarching goal of IIOE-2, which is to “… advance our understanding of interactions among geologic, oceanic and atmospheric processes that give rise to the complex physical dynamics of the Indian Ocean region, and determine how those dynamics affect climate, extreme events, marine biogeochemical cycles, ecosystems and human populations” (Hood et al., 2015).

We investigated ontogenetic variability in feeding and prey selection by Southern Bluefin Tuna larvae (SBT; Thunnus maccoyii) in their only global spawning region, located in the eastern Indian Ocean between northwestern Australia and Indonesia. Zooplankton prey and SBT larvae were sampled during four multi-day Lagrangian experiments conducted in the southern Argo Basin during the peak midsummer spawning season in January–February 2022. The zooplankton were identified, enumerated, sizes measured, and their developmental stages ascertained both in situ and from the stomach contents of the larvae. Larval stomach contents revealed high feeding incidence of 95 % with at least one prey item ingested with an average of 3.9 zooplankton prey per larva. Diet and prey selection transitioned during larval ontogeny from copepod nauplii to calanoid and corycaeid copepodites, and ultimately to cladocerans, as well as fish larvae when these were available. However, for all developmental stages and experiments, appendicularians stood out as the most significant prey taxon, constituting an average of 57 % of prey carbon biomass consumed and up to 79 % for postflexion stages. We observed some indication of increasing selection for appendicularians and fish larvae where they were most abundant, even when other suitable prey items were more readily available. Our study documents unprecedented high feeding incidence and positive selection for appendicularians compared to previous investigations of bluefin species, highlighting a pathway that enhances food web transfer efficiency. Appendicularians are uniquely able to thrive in oligotrophic environments and could be an optimal food source supporting SBT larvae in the future ocean.

Southern Bluefin Tuna (SBT, Thunnus maccoyii) range broadly in rich feeding grounds of the Southern Hemisphere but spawn only in a small tropical region off northwestern Australia directly downstream of the Indonesian Throughflow. Here, we describe goals, physical context, design and major findings of an end-to-end process study conducted during the peak SBT spawning season (January-March 2022) to understand nutrient sources, productivity, pelagic food web structure and their relationships to larval SBT feeding, growth and survival. Mesoscale variability was investigated by continuous underway measurements of surface waters and station sampling along the cruise track. Biogeochemical and community relationships, process rates, and trophic interactions were determined in four multi-day Lagrangian experiments in the southern Argo Basin. The study revealed strong system balances among nitrogen fluxes, phytoplankton production, grazing processes, and export. Highly selective feeding on appendicularians allows efficient trophic transfer from picophytoplankton-dominated production to SBT larvae. Plankton productivity, phytoplankton carbon and zooplankton biomass were proportionately elevated compared to similar measurement from the Atlantic bluefin larval habitat in the Gulf of Mexico, but with less advective input from the coastal margins. Individual-based otolith and stable isotope analyses identify larvae of low trophic position, narrow diet, and narrow maternal diet as the fastest growers most likely to contribute to stock recruitment. Our study highlights the importance of system-level studies to document and understand the subtleties of how food webs of oligotrophic regions respond to climate change, which may not be predictable from the acquired knowledge of historical studies.

Despite playing a critical role in oligotrophic ocean food webs, relatively little is known about the diet of mesopelagic fishes in the Indian Ocean. These fishes are an abundant component of the micronekton assemblages and are a major energy- and nutrient-rich food source, linking the plankton which they feed on to marine predators at higher trophic levels. DNA metabarcoding, a molecular method to identify species from mixed assemblages, has not been commonly used in studies of mesopelagic fish diet, but using it to analyse gut contents can greatly improve the understanding of mesopelagic fish feeding ecology. In this study, we apply DNA metabarcoding (18S rRNA and COI) to gut contents from Stomiiformes and Myctophiformes species from 20 sampling stations covering 30° of latitude on the 110°E meridian in the Indian Ocean. In total, 174 fish specimens from 13 genera were examined. Differences in the gut contents among fish families, geographic areas and fish stages were identified. Specimens within the family Myctophidae had the most diverse diet, more so in the northern sampling stations than the south. Gonostomatidae had the least diverse diet. Overall, the most frequently identified prey items from the gut contents were calanoid copepods and halocyprid ostracods. The proportion of halocyprids were also identified to be significantly different among Myctophidae larvae and juvenile specimens, which is a potential ontogenic shift in diet towards a higher ostracod contribution in juveniles as mouth gape increases. In comparison with other plankton abundance data, Copepoda were the most abundant plankton in the gut contents of all fishes sampled throughout the latitudinal gradient, allowing them to be a potential food resource through the region. There are indications that other less abundant plankton, such as Ostracoda and Malacostraca, may be preferentially targeted by some mesopelagic fish families.

This virtual special issue of Deep-Sea Research II is the sixth volume of scientific papers arising from the Second International Indian Ocean Expedition (IIOE-2, Fig. 1). This diverse body of research from the Indian Ocean includes papers on physical, chemical and biological oceanography, with the latter covering trophic levels from phytoplankton to fish and benthic communities. This volume represents another important step toward achieving the overarching goal of IIOE-2, which is to “… advance our understanding of interactions between geologic, oceanic and atmospheric processes that give rise to the complex physical dynamics of the Indian Ocean region, and determine how those dynamics affect climate, extreme events, marine biogeochemical cycles, ecosystems and human populations” (Hood et al., 2015).

The ‘big old fat fecund female fish’ (BOFFFF) hypothesis suggests that larger, older female fish contribute disproportionately more to the reproductive potential of a stock than smaller, younger female fish. As fishing typically differentially removes larger, mature fish, this can negatively impact reproductive potential and impair the recovery of a depleted stock. In this study, the BOFFFF hypothesis was explored quantitatively for the endemic West Australian dhufish (Glaucosoma hebraicum) by estimating the relationships between total length (TL) of females and spawning season duration, spawning frequency and oocyte size. The impacts of these size effects on estimates of reproductive potential of the G. hebraicum stock were also explored using a per-recruit analysis. Larger (900 mm TL), older mature female G. hebraicum were shown to spawn for a longer duration (six versus two months) and on more occasions (155 versus 60 times) than smaller (350 mm TL), younger mature fish, and thus these larger females have higher annual fecundity. Larger, older mature G. hebraicum also spawn, on average, significantly larger oocytes with greater estimated energy content (474.6 diameter and 0.234 J versus 379.9
and 0.140 J). Due to these size effects, reproductive output of G. hebraicum scales hyperallometrically with fish body mass, rather than isometrically. Not accounting for these size effects in per-recruit analysis resulted in higher estimates of stock reproductive potential and thus stock status. Such overestimates, if used to inform management, have the potential to result in harvest rates being set too high which, in turn, could thus affect stock sustainability.

Dietary and predator–prey studies are more frequently relying on DNA metabarcoding methods, typically achieving results that have a better taxonomic resolution (e.g., species-level) than previous methods. With the continuous advancement in sequencing technology, what was previously accessible only as a large, fixed structure in a laboratory, which had a limited number of users, has now advanced to a small and readily usable device. In this study, we used the gut (content and lining) from juvenile lanternfish (Hygophum) specimens to compare the short-read sequencing capability of the portable Nanopore MinION with the Illumina MiSeq. Primers common in dietary DNA metabarcoding work (COI “Leray primers” and 18S rRNA V4 “Zhan primers”) were used, with an additional comparison of cost-effective COI “Lobo primers” (targeting the same COI fragment) for the proficiency in species detection of a broad range of taxa. Our results indicate high congruency between sequencing machines for, not only taxonomic assignments, but also relative read abundance of the main dietary items. We also identified that Nanopore sequencing is more cost-effective. The Lobo primers are comparable to that of Leray, but substantially reduce the primer set price without compromising detection of taxa. Using both COI and 18S broadened the taxonomic scope, providing greater prey detection. Overall, this preliminary study was successful in creating a foundation for future dietary work involving larvae and transformation stage fishes whereby the content of the gut need not be separated from the gut lining to detect prey. The Hygophum diet detected here aligns with previous research that suggests the main dietary items to be calanoid copepods, but using molecular methods, soft prey was more readily identified compared to studies using visual methods of identification of dietary items. Overall, this study found that Nanopore sequencing is suitable for short-read DNA metabarcoding and can provide rapid access to sequencing results.

We investigated plankton biomass structure, production and grazing rates from temperate to tropical waters (39.5–11.5°S) along the historic 110°E transect in the eastern Indian Ocean (IO) during May–June 2019. The timing captures the seasonal transition from moderate productivity in the subtropical sector to seasonally high primary production in tropical waters as described in IIOE (International Indian Ocean Expedition) studies of the 1960s. Carbon-based estimates of phytoplankton production and microzooplankton grazing were determined from depth profiles of dilution incubations analyzed by flow cytometry and pigments; mesozooplankton biomass and grazing were determined from net sampling and gut fluorescence for the integrated euphotic zone. Phytoplankton biomass varied from 860 to 1740 mg C m−2, averaging 1187 mg C m−2 with no latitudinal trend. Mixed-layer C:Chla ranged from 20 to 40 in the nitrogen-rich subtropical front to 100–180 in tropical waters. Prochlorococcus increased from 141 to 915 mg C m−2 between 39.5°S and 20°S and averaged 700 mg C m−2 at lower latitudes. Synechococcus and photosynthetic eukaryotes contributed least to biomass (3.6 and 30.5%, respectively) at mid-transect locations (15.5–27.5°S). Dinoflagellates and diatoms were typically rare (28 and 6 mg C m−2, respectively). Among heterotrophs, bacteria averaged 476 mg C m−2, with a subtropical front maximum but no latitudinal trend; ciliates averaged 112 mg C m−2, and mesozooplankton increased significantly south-to-north (131–488 mg C m−2). Phytoplankton production and grazing averaged 466 and 461 mg C m−2 d−1, respectively, based on the sums for flow-cytometry measured populations, and 618 and 604 mg C m−2 d−1, respectively, based on Chla-determined rates. Our results highlight key relationships that link stocks and process rates across oceanographic provinces of the eastern IO. Production and grazing increased 6–8 fold from south to north. Prochlorococcus dominated productivity, and microzooplankton accounted for 85–89% of grazing. Production and grazing were strongly coupled and balanced on average. Over the transect, increasing growth conditions (light and temperature) mainly manifested as more rapid biomass turnover and mesozooplankton biomass accumulation.

The large, tropical oligotrophic gyres of the world's oceans are understood to be relatively unproductive, with low phytoplankton and zooplankton biomass, and inefficient food webs, although data are scarce. Here we investigate changes in the zooplankton assemblage along a 15 °C temperature gradient from 20 stations on the 110°E transect as part of the second International Indian Ocean Expedition. To ensure that we reflect most of the zooplankton biodiversity, we used a 100 μm mesh net to capture the small copepod and microzooplankton components that are important and often overlooked in tropical systems. Further, to obtain a synoptic view, we towed the Continuous Plankton Recorder between stations across 30° of latitude. We found that copepod assemblages clustered into four groups, with the most distinct being at the highest latitudes south of the sub-tropical Front. As the ocean temperature increased from south to north along the transect, zooplankton abundance and diversity also increased. The dominant copepod species changed accordingly and were predominantly those with the ability and/or preference to selectively feed on microzooplankton. Although copepods were the most abundant taxon, the proportion of microzooplankton, particularly, mixotrophic Rhizaria, was consistently high. Thus, our study found a highly mixotrophic system supporting secondary production in the oligotrophic Indian Ocean.